Ocarina of Time
Chrono Trigger
FF6
DKC2
Secret of Mana

Ermmm, hmmm. This is too hard, there's too much awesome game music to choose a definite top 5. Far too much.

Well, I'll try. Here's mine, in no particular order... but screw it, I'm listing franchises, not individual games, otherwise I wouldn't be able to choose at all. :p

- Okami
- Zelda
- Mario
- Banjo-Kazooie
- Kirby

... Can't we make a top 10? :p

Here's my top 5, each with my favorite track in the OST (click on the boxart).

1. Super Mario Galaxy

2. Sonic & Knuckles

3. Sonic the Hedgehog 2

4. Super Mario World

5. Metroid Prime

1. Suikoden II
2. Final Fantasy Tactics
3. Shadow of the Colossus
4. Persona 4
5. Either Pokemon Blue, FF8, God of War, The Sims or Chrono Cross

as i recall,, the killzone games had great music in them. the best is iron storm for the saturn. i knew a guy in college who used to play it through his stereo all the time. i really liked the score of it, and i teased the hell out of him for being such a geek. get some real music, fag.

1. frog's theme (chrono trigger, ds)
2. battle (chrono trigger, snes)
3. seaside town (super mario rpg, snes)
4. title screen (New Super Mario Bros Wii, wii)
5. cradle under the star (clock tower, snes)

for overall in game
1. Chrono Trigger (snes)
2. Super Mario Rpg (snes)
3. New Super Mario Bros Wii (wii)
4. TLOZ: Twiligh Princess (wii/gc)
5. TLOZ: A link to the past (snes)
Clock tower (snes) has only one song so I didn't put it here

1. Lineage 2
2. WoW
3. FF6
4. Dragon Age
5. Aion

No. I see you haven't played ALttP and OoT, otherwise you would know that besides 1 or 2 songs, the soundtrack has nothing to do with each other. Play the games first.

I'm really considering the whole soundtrack of a game and not just a couple of good musics (like the list made by VGC )

Final Fantasy X
Donkey Kong Country (Mostly the second)
Dark Cloud 2 Example
Uncharted 2 (I was seriously amazed)
Persona 3 Example

I've been listening to video game music a ton recently, so I suppose I'll contribute to this.

Choosing the top 5 soundtracks for all videogames is pretty much impossible for me, so I'll limit places to one per series (or composer, even). Actually, since it's only 5, I'll also try to list what other people will probably miss. I won't order them, either, that's another impossible task...

Heroes of Might and Magic III:
The Heroes series has amazing music. If you haven't played or heard of these games, do look into it (now!), especially if you're a fan of turn based games. I see many people at VGC seem to play either primarily Japanese games, or Console games. These people need to give Heroes a shot, you won't regret it! I'm considering making a thread later, just for this purpose...
Fav tracks: Combat 2, Rampart Town, Stronghold Town, Rough

Warcraft II - Tides of Darkness:
Something about the older game music really gets to me. Warcraft II's soundtrack really nails the feeling of war, just give it a listen. It has so much oomph in it, it's ridiculous. This is the start of Blizzard's dominance for ya.
Fav tracks: Human 2, Orc 3

Phoenix Wright Series (T&T beng the fav):
These games would not have worked nearly as well without the amazing music. T&T music was done by the composer of Grandia (which has been given 3 mentions in the thread already, surprisingly). He's done the Miles Edgeworth game as well, can't wait for it to come stateside.
Fav tracks: Objection, Cornered, Announce the Truth (from JFA, just had to include this)

Jet Set Radio:
What would this game be without its crazy soundtrack?
Fav tracks: Humming the Bassline, Funky Radio, Let Mom Sleep, Mischievous Boy

Mega Man 2:
He ain't called "Rockman" in Japan for nothin! Easily some of the best music on the NES in this game.
Fav Tracks: Metal Man, Quick Man, Wily 1, Air Man, Bubble Man, Flash Man

Well, that's 5. Too small of a limit for me to be satisfied with my list! Of course, since I also love all of the obvious choices (FFs, Zeldas, Chrono Trigger, etc), I just let others list them for me.