The Doom 3heavy theme. Reason being that besides the startup, you'll only ever hear it again when you're victorious, and almost invariably at the end of any Doom 3 mod episode too. It's sort of like an awesome music of crowning.
The music from MAP14 (Steel Works) may not be the best song ever (mainly because it's a short, cool sounding riff surrounded by several minutes of dull bass), but its remix by TheWeekle manages to make it epic.
Doom 64 may not have much in the way of rocking tunes (only the opening and ending themes could be considered traditional music), but what it does have is an incredibly creepy and atmospheric ambiance that really helps set it as the most Survival Horror-y game in the series until Doom 3 came along (especially when you reach Hell). Here's one of the creepier stage themes if you need an example.
ZX Spectrum home port makes you wish you had that music on original version.
"Nobody Told Me About Id" is so good, it was used for the super secret level of The Plutonia Experiment and gets a new remix for every community-made sequel for it. So far we have Nobody Told Me About Plutonia for Plutonia 2 and I Already Know About Id for Plutonia Revisited. The latter is actually a remake of the SNES version of "Nobody Told Me About Id", though this doesn't detract from the awesomeness.