I just resolved some very frustrating issues that I was having with my retroarch.cfg joystick config file. Default behavior was strange in some of the emulators, and I couldn’t quite get input_enable_hotkey_btn and input_exit_emulator_btn to work correctly. NeoGeo emulation using FBA did work for some crazy reason, but the other emulators did not. When I removed the input_enable_hotkey_btn line from the config, it would exit whenever I pressed button 0 instead of the button that I tried to configure to the cfg file. I ended up restarting from scratch, and seeing the difference between my old config files and the new config files to find out the difference.

My first error was piping instead of appending when I used the retroarch-joyconfig program found in RetroPie/emulators/RetroArch/tools.

What I typed was:
./retroarch-joyconfig | ~/RetroPie/configs/all/retroarch.cfg

I should have typed:
./retroarch-joyconfig >> ~/RetroPie/configs/all/retroarch.cfg

I then compounded my problem by manually copying and pasting the following lines into my config file (using vim over ssh, if I remember correctly):

input_enable_hotkey_btn = "8"
input_exit_emulator_btn = “9″

I had not realized two things:
My config doesn’t need the quotes.
I had accidentally pasted two different types of quotes (“ and ″) into a config file, which likely caused the program to freak out and not read the configuration properly.

After loading RetroPie 1.9.1 onto the card from scratch, I noticed the error of my ways, updated the configuration file correctly, and I am now able to exit emulators effectively and continue to play games.

Learn from my lesson, RetroPie users! Beware the quotes!

Quoted below is my working config file for a Logitech Dual Action USB controller:

## Skeleton config file for RetroArch

# Save all save files (*.srm) to this directory. This includes related files like .bsv, .rtc, .psrm, etc ...
# This will be overridden by explicit command line options.
# savefile_directory =

# Save all save states (*.state) to this directory.
# This will be overridden by explicit command line options.
# savestate_directory =

# Automatically saves a savestate at the end of RetroArch's lifetime.
# The path is $SRAM_PATH.auto.
# RetroArch will automatically load any savestate with this path on startup if savestate_auto_load is set.
# savestate_auto_save = false
# savestate_auto_load = true

# Load libretro from a dynamic location for dynamically built RetroArch.
# This option is mandatory.

# If a directory, RetroArch will look through the directory until it finds an implementation
# that appears to support the extension of the ROM loaded.
# This could fail if ROM extensions overlap.
# libretro_path = "/path/to/libretro.so"

# Path to core options config file.
# This config file is used to expose core-specific options.
# It will be written to by RetroArch.
# A default path will be assigned if not set.
# core_options_path =

# Path to ROM load history file.
# RetroArch keeps track of all ROMs loaded in RGUI and from CLI directly for convenient quick loading.
# A default path will be assigned if not set.
# game_history_path =

# Number of entries that will be kept in ROM history file.
# game_history_size = 100

# Sets the "system" directory.
# Implementations can query for this directory to load BIOSes, system-specific configs, etc.
system_directory = /home/pi/RetroPie/emulatorcores/

# Sets start directory for RGUI ROM browser.
# rgui_browser_directory =

# Sets start directory for RGUI config browser.
# rgui_config_directory =

# Show startup screen in RGUI.
# Is automatically set to false when seen for the first time.
# This is only updated in config if config_save_on_exit is set to true, however.
# rgui_show_start_screen = true

# Flushes config to disk on exit. Useful for RGUI as settings can be modified.
# Overwrites the config. #include's and comments are not preserved.
# config_save_on_exit = false

#### Video

# Video driver to use. "gl", "xvideo", "sdl"
# video_driver = "gl"

# Which OpenGL context implementation to use.
# Possible ones for desktop are: glx, x-egl, kms-egl, sdl-gl, wgl.
# By default, tries to use first suitable driver.
# video_gl_context =

# Windowed xscale and yscale
# (Real x res: base_size * xscale * aspect_ratio, real y res: base_size * yscale)
# video_xscale = 3.0
# video_yscale = 3.0

# Fullscreen resolution. Resolution of 0 uses the resolution of the desktop.
# video_fullscreen_x = 0
# video_fullscreen_y = 0

# Start in fullscreen. Can be changed at runtime.
# video_fullscreen = false

# If fullscreen, prefer using a windowed fullscreen mode.
# video_windowed_fullscreen = true

# Which monitor to prefer. 0 (default) means no particular monitor is preferred, 1 and up (1 being first monitor),
# suggests RetroArch to use that particular monitor.
# video_monitor_index = 0

# Forcibly disable composition. Only works in Windows Vista/7 for now.
# video_disable_composition = false

# Video vsync.
# video_vsync = true

# Attempts to hard-synchronize CPU and GPU. Can reduce latency at cost of performance.
# video_hard_sync = false

# Sets how many frames CPU can run ahead of GPU when using video_hard_sync.
# Maximum is 3.
# video_hard_sync_frames = 0

# Inserts a black frame inbetween frames.
# Useful for 120 Hz monitors who want to play 60 Hz material with eliminated ghosting.
# video_refresh_rate should still be configured as if it is a 60 Hz monitor (divide refresh rate by 2).
# video_black_frame_insertion = false

# Use threaded video driver. Using this might improve performance at possible cost of latency and more video stuttering.
# video_threaded = false

# Smoothens picture with bilinear filtering. Should be disabled if using pixel shaders.
video_smooth = false

# Forces rendering area to stay equal to game aspect ratio or as defined in video_aspect_ratio.
# video_force_aspect = true

# Only scales video in integer steps.
# The base size depends on system-reported geometry and aspect ratio.
# If video_force_aspect is not set, X/Y will be integer scaled independently.
# video_scale_integer = false

# A floating point value for video aspect ratio (width / height).
# If this is not set, aspect ratio is assumed to be automatic.
# Behavior then is defined by video_aspect_ratio_auto.
video_aspect_ratio = 1.33

# If this is true and video_aspect_ratio is not set,
# aspect ratio is decided by libretro implementation.
# If this is false, 1:1 PAR will always be assumed if video_aspect_ratio is not set.
# video_aspect_ratio_auto = false

# Forces cropping of overscanned frames.
# Exact behavior of this option is implementation specific.
# video_crop_overscan = true 

# Path to shader. Shader can be either Cg, CGP (Cg preset) or XML/GLSL format if support is enabled.
# video_shader = "/path/to/shader.{cg,cgp,shader}"

# Load video_shader on startup.
# Other shaders can still be loaded later in runtime.
# video_shader_enable = false

# Defines a directory where shaders (Cg, CGP, XML) are kept for easy access.
# video_shader_dir =

# CPU-based filter. Path to a bSNES CPU filter (*.filter)
# video_filter =

# Path to a TTF font used for rendering messages. This path must be defined to enable fonts.
# Do note that the _full_ path of the font is necessary!
# video_font_path = 

# Size of the TTF font rendered.
# video_font_size = 48

# Attempt to scale the font to fit better for multiple window sizes.
# video_font_scale = true

# Enable usage of OSD messages.
# video_font_enable = true

# Offset for where messages will be placed on screen. Values are in range 0.0 to 1.0 for both x and y values. 
# [0.0, 0.0] maps to the lower left corner of the screen.
# video_message_pos_x = 0.05
# video_message_pos_y = 0.05

# Color for message. The value is treated as a hexadecimal value.
# It is a regular RGB hex number, i.e. red is "ff0000".
# video_message_color = ffffff

# Video refresh rate of your monitor.
# Used to calculate a suitable audio input rate.
# video_refresh_rate = 59.95

# Allows libretro cores to set rotation modes.
# Setting this to false will honor, but ignore this request.
# This is useful for vertically oriented games where one manually rotates the monitor.
# video_allow_rotate = true

# Forces a certain rotation of the screen.
# The rotation is added to rotations which the libretro core sets (see video_allow_rotate).
# The angle is <value> * 90 degrees counter-clockwise.
# video_rotation = 0

#### Audio

# Enable audio.
# audio_enable = true

# Audio output samplerate.
audio_out_rate = 48000

# Audio driver backend. Depending on configuration possible candidates are: alsa, pulse, oss, jack, rsound, roar, openal, sdl, xaudio.
audio_driver = alsathread

# Override the default audio device the audio_driver uses. This is driver dependant. E.g. ALSA wants a PCM device, OSS wants a path (e.g. /dev/dsp), Jack wants portnames (e.g. system:playback1,system:playback_2), and so on ...
# audio_device =

# External DSP plugin that processes audio before it's sent to the driver.
# audio_dsp_plugin =

# Will sync (block) on audio. Recommended.
# audio_sync = true

# Desired audio latency in milliseconds. Might not be honored if driver can't provide given latency.
# audio_latency = 64

# Enable experimental audio rate control.
# audio_rate_control = true

# Controls audio rate control delta. Defines how much input rate can be adjusted dynamically.
# Input rate = in_rate * (1.0 +/- audio_rate_control_delta)
# audio_rate_control_delta = 0.005

# Audio volume. Volume is expressed in dB.
# 0 dB is normal volume. No gain will be applied.
# Gain can be controlled in runtime with input_volume_up/input_volume_down.
# audio_volume = 0.0

#### Input

# Input driver. Depending on video driver, it might force a different input driver.
# input_driver = sdl

# Joypad driver. (Valid: linuxraw, sdl, dinput)
# input_joypad_driver =

# Defines axis threshold. Possible values are [0.0, 1.0]
# input_axis_threshold = 0.5

# Path to input overlay
# input_overlay =

# Overlay opacity
# input_overlay_opacity = 1.0

# Overlay scale
# input_overlay_scale = 1.0

# Enable input auto-detection. Will attempt to autoconfigure
# joypads, Plug-and-Play style.
# input_autodetect_enable = true

# Directory for joypad autoconfigs (PC).
# If a joypad is plugged in, that joypad will be autoconfigured if a config file
# corresponding to that joypad is present in joypad_autoconfig_dir.
# Input binds which are made explicit (input_playerN_*_btn/axis) will take priority over autoconfigs.
# Autoconfigs can be created with retroarch-joyconfig, manually, or with a frontend.
# Requires input_autodetect_enable to be enabled.
# joypad_autoconfig_dir =

# Enable debug input key reporting on-screen.
# input_debug_enable = false

# Sets which libretro device is used for a player.
# Devices are indentified with a number.
# This is normally saved by RGUI.
# Device IDs are found in libretro.h.
# These settings are overridden by explicit command-line arguments which refer to input devices.
# None: 0
# Joypad (RetroPad): 1
# Mouse: 2
# Keyboard: 3
# Generic Lightgun: 4
# Joypad w/ Analog (RetroPad + Analog sticks): 5
# Multitap (SNES specific): 257
# Super Scope (SNES specific): 260
# Justifier (SNES specific): 516
# Justifiers (SNES specific): 772

# input_libretro_device_p1 =
# input_libretro_device_p2 =
# input_libretro_device_p3 =
# input_libretro_device_p4 =
# input_libretro_device_p5 =
# input_libretro_device_p6 =
# input_libretro_device_p7 =
# input_libretro_device_p8 =

# Keyboard input. Will recognize normal keypresses and special keys like "left", "right", and so on.
# Keyboard input, Joypad and Joyaxis will all obey the "nul" bind, which disables the bind completely, 
# rather than relying on a default.
# input_player1_a = x
# input_player1_b = z
# input_player1_y = a
# input_player1_x = s
# input_player1_start = enter
# input_player1_select = rshift
# input_player1_l = q
# input_player1_r = w
# input_player1_left = left
# input_player1_right = right
# input_player1_up = up
# input_player1_down = down
# input_player1_l2 =
# input_player1_r2 =
# input_player1_l3 =
# input_player1_r3 =

# Two analog sticks (DualShock-esque).
# Bound as usual, however, if a real analog axis is bound,
# it can be read as a true analog.
# Positive X axis is right, Positive Y axis is down.
input_player1_joypad_index = 0
input_player1_b_btn = 1
input_player1_y_btn = 0
input_player1_select_btn = 8
input_player1_start_btn = 9
input_player1_up_axis = -5
input_player1_down_axis = +5
input_player1_left_axis = -4
input_player1_right_axis = +4
input_player1_a_btn = 2
input_player1_x_btn = 3
input_player1_l_btn = 4
input_player1_r_btn = 5
input_player1_l2_btn = 6
input_player1_r2_btn = 7
input_player1_l3_btn = 10
input_player1_r3_btn = 11
input_player1_l_x_plus_axis = +0
input_player1_l_x_minus_axis = -0
input_player1_l_y_plus_axis = +1
input_player1_l_y_minus_axis = -1
input_player1_r_x_plus_axis = +2
input_player1_r_x_minus_axis = -2
input_player1_r_y_plus_axis = +3
input_player1_r_y_minus_axis = -2
input_enable_hotkey_btn = 8
input_exit_emulator_btn = 9

# If desired, it is possible to override which joypads are being used for player 1 through 8.
# First joypad available is 0.
input_player1_joypad_index = 0
# input_player2_joypad_index = 1
# input_player3_joypad_index = 2
# input_player4_joypad_index = 3
# input_player5_joypad_index = 4
# input_player6_joypad_index = 5
# input_player7_joypad_index = 6
# input_player8_joypad_index = 7

# Joypad buttons.
# Figure these out by using RetroArch-Phoenix or retroarch-joyconfig.
# You can use joypad hats with hnxx, where n is the hat, and xx is a string representing direction. 
# E.g. "h0up"
# input_player1_a_btn = 0
# input_player1_b_btn = 1
# input_player1_y_btn = 3
# input_player1_x_btn = 2
# input_player1_start_btn = 7
# input_player1_select_btn = 6
# input_player1_l_btn = 4
# input_player1_r_btn = 5
# input_player1_left_btn =
# input_player1_right_btn =
# input_player1_up_btn =
# input_player1_down_btn =
# input_player1_l2_btn =
# input_player1_r2_btn =
# input_player1_l3_btn =
# input_player1_r3_btn =

# Axis for RetroArch D-Pad. 
# Needs to be either '+' or '-' in the first character signaling either positive or negative direction of the axis, then the axis number. 
# Do note that every other input option has the corresponding _btn and _axis binds as well; they are omitted here for clarity.
# input_player1_left_axis = -0
# input_player1_right_axis = +0
# input_player1_up_axis = -1
# input_player1_down_axis = +1

# Holding the turbo while pressing another button will let the button enter a turbo mode
# where the button state is modulated with a periodic signal.
# The modulation stops when the button itself (not turbo button) is released.
# input_player1_turbo =

# Describes the period and how long of that period a turbo-enabled button should behave.
# Numbers are described in frames.
# input_turbo_period = 6
# input_turbo_duty_cycle = 3

# This goes all the way to player 8 (*_player2_*, *_player3_*, etc), but omitted for clarity.
# All input binds have corresponding binds for keyboard (none), joykeys (_btn) and joyaxes (_axis) as well.

# Toggles fullscreen.
# input_toggle_fullscreen = f

# Saves state.
# input_save_state = f2
# Loads state.
# input_load_state = f4

# State slots. With slot set to 0, save state name is *.state (or whatever defined on commandline).
# When slot is != 0, path will be $path%d, where %d is slot number.
# input_state_slot_increase = f7
# input_state_slot_decrease = f6

# Toggles between fast-forwarding and normal speed.
# input_toggle_fast_forward = space

# Hold for fast-forward. Releasing button disables fast-forward.
# input_hold_fast_forward = l

# Key to exit emulator cleanly. 
# Killing it in any hard way (SIGTERM, SIGKILL, etc, will terminate emulator without saving RAM, etc.)
input_exit_emulator = escape

# Applies next and previous XML/Cg shader in directory.
# input_shader_next = m
# input_shader_prev = n

# Hold button down to rewind. Rewinding must be enabled.
input_rewind = r

# Toggle between recording and not.
# input_movie_record_toggle = o

# Toggle between paused and non-paused state
# input_pause_toggle = p

# Frame advance when game is paused
# input_frame_advance = k

# Reset the game.
# input_reset = h

# Configures DSP plugin
# input_dsp_config = c

# Cheats.
# input_cheat_index_plus = y
# input_cheat_index_minus = t
# input_cheat_toggle = u

# Mute/unmute audio
# input_audio_mute = f9

# Take screenshot
# input_screenshot = f8

# Netplay flip players.
# input_netplay_flip_players = i

# Hold for slowmotion.
# input_slowmotion = e

# Enable other hotkeys.
# If this hotkey is bound to either keyboard, joybutton or joyaxis,
# all other hotkeys will be disabled unless this hotkey is also held at the same time.
# This is useful for RETRO_KEYBOARD centric implementations
# which query a large area of the keyboard, where it is not desirable
# that hotkeys get in the way.

# Alternatively, all hotkeys for keyboard could be disabled by the user.
# input_enable_hotkey =

# Increases audio volume.
# input_volume_up = kp_plus
# Decreases audio volume.
# input_volume_down = kp_minus

# Toggles to next overlay. Wraps around.
# input_overlay_next =

# Toggles eject for disks. Used for multiple-disk games.
# input_disk_eject_toggle =

# Cycles through disk images. Use after ejecting.
# Complete by toggling eject again.
# input_disk_next =

# Toggles RGUI menu.
# input_menu_toggle = f1

# Toggles mouse grab. When mouse is grabbed, RetroArch hides the mouse,
# and keeps the mouse pointer inside the window to allow relative mouse games
# to work better.
# input_grab_mouse_toggle = f11

#### Misc

# Enable rewinding. This will take a performance hit when playing, so it is disabled by default.
rewind_enable = true

# Rewinding buffer size in megabytes. Bigger rewinding buffer means you can rewind longer.
# The buffer should be approx. 20MB per minute of buffer time.
rewind_buffer_size = 10

# Rewind granularity. When rewinding defined number of frames, you can rewind several frames at a time, increasing the rewinding speed.
rewind_granularity = 2

# Pause gameplay when window focus is lost.
# pause_nonactive = true

# Autosaves the non-volatile SRAM at a regular interval. This is disabled by default unless set otherwise.
# The interval is measured in seconds. A value of 0 disables autosave.
# autosave_interval =

# When being client over netplay, use keybinds for player 1.
# netplay_client_swap_input = false

# Path to XML cheat database (as used by bSNES).
# cheat_database_path =

# Path to XML cheat config, a file which keeps track of which
# cheat settings are used for individual games.
# If the file does not exist, it will be created.
# cheat_settings_path =

# Directory to dump screenshots to.
# screenshot_directory =

# Records video after CPU video filter.
# video_post_filter_record = false

# Records output of GPU shaded material if available.
# video_gpu_record = false

# Screenshots output of GPU shaded material if available.
# video_gpu_screenshot = true

# Block SRAM from being overwritten when loading save states.
# Might potentially lead to buggy games.
# block_sram_overwrite = false

# When saving a savestate, save state index is automatically increased before
# it is saved.
# Also, when loading a ROM, the index will be set to the highest existing index.
# There is no upper bound on the index.
# savestate_auto_index = false

# Slowmotion ratio. When slowmotion, game will slow down by factor.
# slowmotion_ratio = 3.0

# The maximum rate at which games will be run when using fast forward. (E.g. 5.0 for 60 fps game => 300 fps cap).
# RetroArch will go to sleep to ensure that the maximum rate will not be exceeded.
# Do not rely on this cap to be perfectly accurate.
# A negative ratio equals no FPS cap.
# fastforward_ratio = -1.0

# Enable stdin/network command interface.
# network_cmd_enable = false
# network_cmd_port = 55355
# stdin_cmd_enable = false

# input_enable_hotkey_btn = 6
# input_exit_emulator_btn = 7
# input_rewind_btn = 3
# input_save_state_btn = 4
# input_load_state_btn = 5
# input_player2_a_btn = 0
# input_player2_b_btn = 1
# input_player2_x_btn = 2
# input_player2_y_btn = 3
# input_player2_l_btn = 4
# input_player2_r_btn = 5
# input_player2_start_btn = 7
# input_player2_select_btn = 6
# input_player2_left_axis = -0
# input_player2_right_axis = +0
# input_player2_up_axis = -1
# input_player2_down_axis = +1