Alright, I’m just figuring this out myself. First, make sure you’re running cripsy doom 2.3 Cripsy-Doom_2.3. Install like so:

sudo apt-get install -y libsdl1.2debian libsdl-image1.2 libsdl-mixer1.2 libsdl-net1.2 timidity
wget -P /tmp/ http://misapuntesde.com/res/crispy-doom_2.3_armhf.deb
sudo dpkg -i /tmp/crispy-doom_2.3_armhf.deb

Then copy your wad files somewhere handy. I make a directory called ‘wads’ in /home/pi/ and put the wads in there. Then run cripsy like so:
crispy-doom -iwad ~/wads/doom.wad
Let it load up – it’ll create the config files we need to change. Then exit the game. Next, you’ll need to turn on joystick support:
nano ~/.crispy-doom/default.cfg
Look for a line that reads “use_joystick 0” and change the 0 to 1. Save
Next, you’ll need to tell crispy-doom about your joystick:
nano ~/.crispy-doom/crispy-doom.cfg
Look for a line that says ‘joystick-index -1’. In my case, my xbox 360 controller is joystick 0, so I changed the -1 to a 0. Then look at the lines below. For my controller, I wanted forward-back and strafe on the left joystick, and turn left/right on the right joystick, so I set the following values:

joystick_index                0
joystick_x_axis               2
joystick_x_invert             0
joystick_y_axis               1
joystick_y_invert             0
joystick_strafe_axis          0
joystick_strafe_invert        0

I’m still fussing around with the buttons – the default seems to be to have the bottom (A) fire, and the top (Y) button open the doors. Still working on the details there, but I hope this is enough to get you started.

EDIT: I got the buttons the way I wanted them but now I’m looking for a way to quit out of the game with the joystick. I can hit the menu button, select quit from the menu, but the game comes up and wants me to type Y to exit… too bad there’s no Y key on the joystick. Hoping someone has a bright idea. :)