Alias files, in gmenux2 and gmenunx, are files that tell the file selector to replace one filename with another when displaying the ROM name. Originally meant for MAME and Neo-Geo ROMS, they're also useful for use with no-intro compatible ROM collections, allowing one to have intact filenames (retroarch coverart uses nointro filenames, for example) while still having human-readable game names.
To use an alias file, find your emulator core under /mnt/gmenu2x/sections/emulators/, and add a line to the config file
aliasfile=/mnt/PATH_TO_INTRO_FILE. (if you're lame, you can also set it from the GUI).
Pre-created alias files for Neo-Geo and MAME exist, but I wrote a simple bash script to generate alias files for your personal collection (assuming the file names are in accordance with the no-intro standard) cd into the directory your ROMs are in, and run the command
You probably don't want to run my awful bash command (it screws up on a few special characters), so I went ahead and generated a GBA alias file and posted it here