Some copies of the id Anthology version contain an updated Final Doom; the rest uses the original. The GOG.com release uses this alternate version.
All patches for the retail versions of Final Doom (as well as Doom and Doom II: Hell on Earth) can be found here.
Since the release of the engine's source code, various source ports have been released. See the link above for details and recommendations.
Run the program as administrator
The yellow keycard in MAP31: Pharaoh from TNT: Evilution is missing due to it being accidentally flagged as a multiplayer-only item, making it impossible to complete the level with 100% completion without resorting to cheats.
DOOM2.EXE -file TNT.WAD TNT31.WAD
DOOM2.EXE -file TNT.WAD