Dunno if it's my absolute favorite, but MMX4 is way up there. I absolutely love the synth sounds they used.
Some others I just adore:
Too lazy to link all, but here are some others that popped into my head while reading through this thread:
Phantasy Star Online, Super Mario 64, other Final Fantasy games (I, IV, V, VI, VIII, IX, X etc.), Super Meat Boy, Ducktales, MM3, Soldier Blade, Triggerheart Excelica, Sonic 3 & Knuckles, Castlevania: Chi No Rondo and Circle of the Moon and Mass Effect (best space ambient I've ever heard).