I think mine would be the super mario underground theme,and the song of storms those two are my favorite.

 The Smashing Live CD is awesome, basically it's all the music from Super Smash Bros. Melee. My favorite is Great Bay Shrine which incorporates the main theme from the Legend of Zelda games. I hope they come out with an easier to find soundtrack for Brawl. 

 You really can't go wrong with any CD with the words "Final Fantasy" and "orchestral" in it. Liberi Fatali from the FFVIII OST and One Winged Angel from 'FFVII - Reunion' really deserve special mention for making a huge leap in the quality and scale of video game music.

 I also loooooooove the theme from Metal Gear Solid 2 and the music from the trailer to Warcraft III. OUTSTANDING pieces, made oddly enough as promotional material.

And of course the music from Warrior Epic is totally awesome too.  

Eons ago there was a SNES game called Plok with music so good that when I started the game I mistakenly thought the sound was coming from a television show or movie.

Mm. I'm a fan of the orchestral version of One Winged Angel, myself.    I'd also like to point out the awesomeness of "Small of Two Pieces" (sometimes translated as "Small Two of Pieces" -- I'm not sure which is more accurate) , an amazingly haunting song from the closing credits of Xenogears.

 I love the intro to Chrono Trigger, and the whole Soundtrack for Lunar Silver Star Story is great, I some times just listen to that while I play other games : P

I love Kingdom Heart's Dearly Beloved, and a song in Halo 2(in a room full of hunters methinks) 

Hmm. Hard choice.

Overlooking music games, I really enjoyed the music from FFVI. Some of the Zelda music really sticks out in my mind, such as Midna's Lament, Ballad of the Windfish, etc. I enjoy the sublety of the Animal Crossing music, if you count it.  Advance Wars is also a favorite for music.
For something, y'know, outside of Nintendo, I find MGS to have an awesome Soundtrack. 

Overall, I don't think I can really choose -just one- or something. D: 

 I would have to say Dreadlocks in Madden 08. Only song I can actually remember in Madden 08 and its so pointless all it talks about is dreadlocks.

 Halo, Mario them, mario invincible music and some of the FFVII stuff

i would say halo and FF

Halo,Mario Theme and Zelda

 lets not forget the game music from "guitar hero" lol 

dude, pokemon music.  Pokemon red/blue and silver/gold/crystal are the best ever.

C&C Red alert (original red alert not RA2) The music meshed perfectly with the game.

Theres so many good ones, but another I remember being really good is Warcraft 2 (plus WC2 expantions hidden track is just pwnage :P).

 Another thing i'd like to add which is more or less the same topic is the best music I found to go with a specific game, that isn't in or made for the game. Amon Amarth+Medieval 2 Total War, it's like they were made for eachother, it's just the perfect blend of music and gameplay! Plus most the songs fit right in as your playing the game, so it's possible to create a huge playlist that fits perfectly into the game rather than 1 song being awesome with a game which would get old fast. If it wern't for that combination of music and the game I found, I doub't I would have lasted as long as I did in the game, its kind of one of those, play it once, play it twice, might as well have played it a million times games.