I can't believe no one mentioned Super Mario Bros.

Best soundtrack: Castlevania III
Best individual pieces: Castlevania

There are a ton of games with awesome music on NES though. I agree with most/all of those mentioned.

At the risk of sounding generic:

Just for fun - though off topic

Old School Soundtracks (top to bottom)
NES: Journey to Silias, Mega Man 2
SNES: Actraiser, Donkey Kong Country
Genny: Streets of Rage, Sonic 1

Old School Themes (singles)
NES: SMB and Zelda (Kondo is the man)
SNES: Various tracks from Rock and Roll Racing
Genny: Final Showdown from Streets of Rage 2 (Yuzo is also the man)

I really liked the final boss song from Double Dragon 3 on the NES, when the third mummy changes into the princess. It is so dramatic, you knew that you were facing great dangers with that song.

http://youtube.com/watch?v=dwjFXGM9F1c&feature=related

I really would like to hear a remix from this, it could be so great.

ZELDA 2 the Adventure of Link is my pick.

Zelda 2 Temple theme

Castlevania 2 (Bloody Tears goldammit!)

Bionic Commando

Mega Man 2

Metroid

I like Blaster Master too

Definitely everything from Konami (or UltraGames at the time). It's too hard to pick one definitive ''best'' soundtrack.

I especially enjoy musics from Gradius, Gradius II, Salamander, TMNT 2: The Arcade Edition, TMNT 3: The Manhattan Project, Castlevania, Contra, Super C and Top Gun: The Second Attack. Classics!

LifeForce was tight.

Even when you died the "game over" music was dope. I reccomend everyone go d/l the rom and play it. Fun game.

The Boss music from Legend of Zelda Ocarina of time for the Death Mountain Levels (especially the intro).
Grass Land's Music from Super Mario Bros 3.
Vanilla Dome theme from Super Mario World.
Spring Yard Zone from Sonic the Hedgehog (has that early 90's old skool feel)
The Banana Cave levels in Donkey Kong Country 3.
Bowser Battles in Super Mario 64.