Recently, I've been playing a bunch of custom Doom wads, and one of the things that stuck out most to me was the breadth and quality of custom soundtracks talented composers would make specifically for those wads. So here is just a small sampling of many of the fantastic MIDIs that dedicated composers made over the years. WAD or Map titles (where applicable) are put after each entry.
Mark Klem - Hidden Anger (Memento Mori)
Jeremy Doyle - Quarry (Icarus: Alien Vanguard)
James Paddock - Sanctified (Plutonia 2)
Petter Mårtensen - Temple of Judgment (Hell Revealed II)
B.P.R.D - The Mucus Flow (The Mucus Flow)
Edit: Here's some more:
Xaser Acheron - Angry Science (Back To Saturn X: Episode 2)
Cammy - Chicago Typography: (Alien Vendetta Community MIDI Pack)
There's also the
MIDI Pack for the Master Levels for Doom 2 by Peter Lawrence, which I cannot link a single track of, because so many of them are so good.
i could link more.