Oh, you've got me started on this!
I'm an avid soundtrack listener, as I try getting tons of soundtracks for the games I love. over 400 tracks on my iPod are soundtrack, no joke. I simply CANNOT limit myself to my top 3.
StarCraft had an 'okay' soundtrack. I'm not criticizing it on the oldness of it, and the use of MIDI.
Red Alert, Red Alert 2, and Yuri's Revenge. I'll go as far to say Universe at War. Why? All of the soundtracks were composed by the exalted Frank Klepacki. Even he used a bit of MIDI in his music. But he did it in such a hard-rocking, bad-ass way that his music simply cannot be overlooked. He doesn't just do the prototypical '90s music, either: in UAW, he does some epic suites for Masari and even the Heirarchy.
Supreme Commander. Jeremy and Julian Soule do a soundtrack of epic proportions here. SupCom has one of the most epic, bombastic (in a good way), rich, and dynamic soundtracks I've ever heard; and I've heard many. The SupCom main theme is used in such a way, you believe it belongs there, not forced in like other soundtracks. (Mass Effect being one of them.) The diversity between factions reflects upon the music, and you have a definite feel for each of them within the music.
Medal of Honor: European Assault. When I first learned that Christopher Lennertz was taking over as the composer for the Medal of Honor series, I braced myself for the absolute worse. And guess what? I was blown away. Right from the beginning of the soundtrack, you don't hear jingoism or patriotism. You hear a unilaterally understood theme of loss, risk, and victory. Dogs of War (initial track) literally brought tears to my eyes. This is a deep soundtrack, while lacking a bit of diversity, as this is a WWII game. It's jsut done with such care and detail, I can not afford to overlook this classic.
Halo 3. I thought I was going to be fed the same crap again, but Marty O'Donnel actually stepped up to the plate, and created a decent soundtrack, featuring more elegant themes and challenging the commonly held idea that piano doesn't belong in a shooter. All I can say is WRONG!
Super Mario Galaxy. I know everyone's going to hate me for this one, but Nintendo's composers (including Mahito Yokota) gave it their all when composing for this game. IF there ever was a benchmark for diversity, this would be it. SMG's soundtrack is one of the most refreshing soundtracks I've heard in a while, forgoing a ham-handed effort at a soundtrack like most developers do, you here elements that are inexplicably right, even though you'd never think there was this or that in the music; it just fits. Tracks ranging from the epic opening to the heart-felt closing, to the fun, vibrant tracks in between, this is a soundtrack to be remembered.
Command & Conquer 3. When Franck Klepacki was off composing with his buddies over at Petroglyph (which composed of former Westwood members), EA needed someone who could fill his shoes for C&C3. I know EA probably wasn't expecting to get such a soundtrack out of Steve Jablonsky (and Trevor Morris), but he went above and beyond their expectations, composing one of the finest electronic albums I've heard.
I'll end my ranting with some others, and honorable mentions:
Star Wars: Republic Commando (Kothe!!! Ratande kothe!!!)
Command & Conquer: Generals (Zero Hour)
Sins of a Solar Empire
Battlefield 2142
Select tracks from LoZ:OoT, WW, and TP
Medal of Honor: Frontlines
SimCity 4 (just breathtaking)