Since making NES music is kind of my specialty now, and it's pretty much all I listen to, I suppose I'll raise from the dead and lay down my 2 cents!
Here are my own personal favourites, in no particular order:
-Shatterhand
-Akumajou Densetsu
-Lagrange Point
-Asterix
-Battletoads
-Erik The Viking (unreleased game, but awesome soundtrack! Download it
here.)
-Gimmick! (the original Famicom version, not the Scandinavian mockery)
-Contra
-Madara
-Silver Surfer
-Street Fighter 2010: The Final Fight (has nothing to do with the well-known 2D fighting franchise!
-Ferrari Grand Prix Challenge
-Exciting Soccer (FDS)
-Exciting Billiard (FDS)
-Exciting Basket (FDS)
-Adventure Island 1/2/3
There are many many more that I probably forget about, and again, those are purely from my own personal favourites. They probably don't qualify as "best soundtracks", but then again, which ones do? It's such a subjective question to answer. What set criteria do you use, how do you avoid bias, etc.
Hopefully there's some of these you didn't know about that you'll discover after reading my post!
By the way, if you're going to listen to those in NSF format, I highly recommend
NSFPlay! </shameless plug>

EDIT: I just saw that this thread was like 3 months old. Sorry about that, I hope my contribution is still considered a useful enough one to warrant bumping. If not feel free to just delete my post and/or lock this thread.