A "compatible" IWAD for 3DGE is either DOOM, DOOM II, PLUTONIA, TNT, HACX, CHEX QUEST, FREEDOOM, or HERETIC.
3DGE will not load any other type of IWAD (strife.wad, etc) because they are not supported in the game engine.
Heretic has issues as support is not finished yet, but the game recognizes this as a valid IWAD nonetheless.
As of this writing, FREEDOOM has entered a Phase 1/Phase 2 branch, which means the IWADs will need to be renamed to doom.wad/doom2.wad, until a new version of 3DGE comes out that will patch this issue.
You can also launch a DOOM 1 or DOOM II PWAD with any IWAD that 3DGE can find at the time, but textures might not display properly, as well as certain sounds/enemies/etc. However, since DDF contains all of the entries for all commercial IWADS, you might get a question mark in place (of say, the Chaingunner) if you are doing this method. This does not apply to IWADS. For example, if you are running a PWAD with MAP01 with the DOOM IWAD loaded, 3DGE will display HELL ON EARTH as an additional episode - though textures will be missing (see below).
If you launch 3DGE with DOOM.wad (the executable will assume DOOM 2 takes precedence) with doom2.wad in the same directory, then you can play both DOOM and DOOM II together (Doom 2's episode appears as HELL ON EARTH), and even use (for example) the DOOM 2 Super Shotgun in the first game. You can also freely warp between MAP/EXMX slots - this also works with TNT and PLUTONIA if they are loaded with Doom 1. PWADS that are for DOOM 2, for example, will load with the DOOM 1 IWAD, but certain textures/patches/monsters will not be present that are a part of DOOM 2 (unless the two IWADS are loaded together).