Favorite game, Eh...
Really tough call. If I had to pick one, it'd be a Zelda. Either A Link To The Past or Ocarina Of Time. I also REALLY liked Twilight Princess. The original Zelda, as mentioned earlier in this thread, was great. I'd easily say that was #1 on the NES for me, FWIW.
But I think Goldeneye really deserves a look, even if for multiplayer alone. We used to play the hell out of that game in high school. The original Mario, as well as Mario 64, for obvious reasons.
I'd say the Madden franchise would be in there. 2008 has been kinda buggy, but overall, that is one constant thing I've played for years.
NBA Jam was always fun. Mortal Kombat... I think #3 was pretty awesome.