You don't NEED multiple copies of prboom installed just to run seperate WAD's... you can instead write a script for each WAD, and then the script will show up in the menu. You kind of need to know how to write Unix shell scripts in order to do this, but here's the gist of it:
Code:
#!/bin/bash
./prboom -iwad doom2.wad -file filename.wad > prboom.log.txt 2>&1
sync
cd /usr/gp2x/
./gp2xmenu
If you paste that text into a text file (with Unix line endings) named "Filename.gpe", then you'll get an icon in your menu with the name "Filename", which will attempt to start prBoom using filename.wad, with Doom 2 as the base. Basically all you'd have to do is change "filename.wad" to whatever the filename is for the WAD you want to use, and save the script with a different filename, and boom, you effectively have a seperate program without wasting a bunch of space.
I use scripts like this on my SD card so that I can run Ultimate Doom, Doom 2, and Final Doom easily. I've never tried the Counterstrike mod, but if it uses extra stuff like Dehacked patches and such, then you need to add other stuff to the command line in the script.
--Zero