Oh, here's a big, and not complete, list (in no particular order):
Final Fantasy specifically FFIX (Uematsu's personal favorite, too), but every game up to 12 was a winner
Metroid The whole series is full of music that is moody and ominous, but energetic when it needs to be.
Guacamelee Best boss music evar! Almost every single track also has a World of the Dead alternate track.
Dark Cloud Listen to that catchy main theme
Halo somehow Martin O'Donnell made Gregorian Chant work as an FPS theme
God of War Absolutely epic and dark, There's a reason why one of my ringtones is GoW2's The End Begins.
Doom obvious (great) ripoffs of heavy metal songs of the day for fast paced action, foreboding pieces to make you uneasy when walking down cramped corridoors (Doom 64's, the real Doom 3, entire soundtrack was ambient, extremely evil sounding stuff.)
Mega Man X (mostly the first game) - Great tracks that fit the futuristic setting and individual level themes
Ecco the Dolphin and Tides of Time - moody, atmospheric (Can you tell I like that kind of music?) Ecco 1 especially gets the moody part right. The Genesis "twang" helped.
Sonic especially Sonic 3 and Knuckles, but the other classics, new compositions, and even the pop music work with him so well
Call of Duty: World at War The Red Army Theme alone wins, but the rest sure didn't need help.
Trine 1 and 2 Some complain about the first game's whimsical and similar sounding songs, but I think it fits the sort a fairy tale vibe of the game. Plus, it new when to pull out the epic and/or foreboding stuff (The Forge). Trine 2 fixed the complaints with a more varied soundtrack.
Okami An exceptional soundtrack with, of course, a traditional Japanese theme; filled with both peaceful, relaxing melodies and ominous leitmotifs
The Legend of Zelda IMHO, each game only has a handful of standout songs, but those themes are something.