I agree on everything you guys mentioned.
I particulary loved SMW2:Yoshi's Island soundtrack, but then again, DK Country, Super Mario RPG, Mario 64 and it goes on and on.
Pilot Wings 64 music was pretty soothing and atmospheric too.

Three games instantly stick out in my mind:

Ocarina of Time
Super Mario Galaxy
Super Smash Bros Brawl

But the third is kind of cheating, so here are my runners up:

Metroid Prime
Lylat Wars
Super Mario 64
Fire Emblem Radiant Dawn
Mario Tennis
Yoshi's Story
Pikmin 2 (If you include Ai no Uta!)

Edit: I forgot to include F-Zero GX - great soundtrack!

IMO All Zelda soundtracks and Super Mario Galaxy.

Super Metroid and The Legend of Zelda: Wind Waker, but it is a tough competition as there are many great pieces in the catalog.

mario galaxy soundtrack is just so great.

Oldschool: DK Jamz
Newschool: Brawl (my favorites being the retro remixes of Kid Icarus, Dr. Mario, Tetris, the oldschool NES medley, the Donkey Kong arcade remix, and pretty much all the Mario/Zelda/F-Zero/classic Sonic stuff)

Galaxy, Windwaker, Endless Ocean come to mind.

OoT as well.

And even though I don't have the game: SSB:Brawl.... I keep humming the theme tune despite never playing it.

I had to think of which stage had the best music in Super Smash Bro. What I came up with is Kirby's stage the fountain of dreams.

DK country 2 hands down. And all other rareware games, but if those dont count because they're rare than I choose MG, SSBB, F-zero and everything from zelda

You're pretty much asking for a laundry list of good OSTs due to the history of Nintendo, but I'll try to limit it to under 10:

1. Kirby's Adventure (NES)
2. Super Mario Bros (NES)
3. Super Mario Bros 3 (NES)
4. Super Mario Galaxy (Wii)
5. The Legend of Zelda (NES)
6. The Legend of Zelda: Links Awakening (GB)
7. The Legend of Zelda: Ocarina of Time (N64)
8. Pokemon Red/Blue (GB/GBA)
9. Super Metroid (SNES)
10. Super Smash Bros Brawl (Wii)