Looks like file system corruption on your SD :-(
It could be possible to recover, have a look in this thread for some suggestions: http://www.raspberrypi.org/forums/viewtopic.php?f=28&t=63798
Otherwise you will have to start again with a new RetroPie setup, I moved to a USB install after my SD card kept corrupting, see this thread for instructions: https://www.petrockblock.com/forums/topic/how-to-run-from-usb-the-best-method/
Another good thing to do is to make regular backups using Win32DiskImager: http://sourceforge.net/projects/win32diskimager/
Hope you can recover it :-)