The Doom 3 heavy 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.
"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.
Suspense is a very tense theme that's perfect for the abandoned Phobos Lab.
Episode 2, Mission 9 (or E-3, M-1 if you never found Episode 2's secret level) literally called "Untitled." Yeah, it's a ripoff of a Pantera song, but it doesn't matter. That riff. Kicks. ASS!
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.