ok.. some WADS will work fine for GP32 since all the graphics are in the WAD itself and there's no fudging of the Doom.exe file with some hacked program (this was used inthe past to extend the abilities of background interactions, sprites capabilities etc..).
However some WADS will play but the graphics will be completely messed up and replaced by that of the main Doom game. A case in point is the Alien Doom WAD where the "straight" file will have all Doom - only textures and all of the object graphics from Doom. This is because when its on a GP32 its missing "links" to the main Doom file through those .DEH and .STR files you sometime might see. An example of this is the sheer amount of candlesticks that are stuck in the corridors of the game (making it unplayable). Whereas in the "fixed" version (on my site) these are replaced with the overhanging lighting graphic. Some of the blocking remains (ie unpassable areas that should be passable) on later levels but will be sorted out in time.
As a general rule, WADS that dont have the annoying DEH or STR files with them will be fine on GP32 as proven with the "Osiris" WAD (from Doom WAD Station), but this is where most "Total Conversions" fall - since they end up rewriting parts of the original game (making objects pass throughable, behaviour of sprites change etc..) and have those ever annoying DEH and STR files.
Pretty much all WADS will run on a GP32, its working out where in the game that the graphics mess up, and then going into the WAD and changing the reference for a new graphic. (and in doing so it will reference itself rather than the main Doom game or IWAD and therefore not require its links with those pesky .DEH and .STR files)
Hope this helps you, and for what its worth Im just a Photoshop/PSPer too!