All custom wads including Total Conversion wads that do not require some extended hacking in the game itself, should work fine with GPDoom.
However, all TC's that either use a changed doom executable or require a .deh (Dehacked, a tool that modified certain aspects in the game to make it behave differently) file to function, are not likely to work well (or at all) with GPDoom as it doesn't support those, as far as I know.
This means that only TC's that replace maps/graphics/sounds/levels are suitable for use, and of course, all other PWAD's that worked with the original Doom games.
Also, the two different WAD types are IWAD and PWAD. The IWAD are the commercial main data files that come with either game. doom1.wad is the shareware data file, doom.wad is the commercial data file for Doom episodes 1 through 3 (Ultimate doom also carries the same file name), and doom2.wad is for Doom 2, of course.
PWAD files are custom files made by fans of Doom, and are only used if they're specified to be used within the game. They can contain the same things that IWAD's do.
So in short, most older TC's and such will work with GPDoom. If they behave erratically, then they likely required some sort of modification to the game or an enchancement of some sort that GPDoom does not support. (See my reply in the Hacx topic).
Of course, do note when you download an TC or a PWAD for which Doom it is meant. Older ones usually work only with Doom (doom 1/ultimate doom) and newer ones are only meant for Doom 2. It's usually specified in an information file that comes along with most such PWAD's.
That's all. I hope this has answered your questions.