If you want to talk about unloved N64 games, you're talking to one of the bigger fans of the first two Turok games. Mario, Zelda, Goldenye, etc. were the best of the bunch, but the death animations, general love of Thunder Lizards and the insanely creative weaponry (Cerebral Bore!) made me love the hell out of the Dinosaur Hunter. Of course, I always used cheats on those games.
Star Wars Racer and Mario Tennis haven't yet been mentioned and deserve a bit of love. Also, you can count me in as someone who appreciated Perfect Dark more than Goldeneye (even if I played more of the latter) due chiefly to weapons such as the aforementioned Laptop Gun as well as the wonder that was the Farsight. Star Fox 64 is probably the best game in that series, even if it did replace the amusing gibberish of the SNES game with horrid voicework.
For those of us who stuck with the game system to the end, Conker's Bad Fur Day was the last hurrah of the N64 and, at the time, a fucking spectacular game. The Xbox version censored the dialogue far more ruthlessly and cut the difficulty in half. For the last days of Nintendo's last cartridge-based console, the graphics were vibrant and full of great effects/animation, the sound effects and score (usually a very weak component of any N64 game) were immersive and spot-on, the multiplayer was ambitious and quite fun (sword decapitations carried over from Jet Force Gemini were always great), and the controls were nearly perfect. The game has aged horribly, mind you, but it was such a fresh and unique experience at that point in time it was like a godsend. I was trudging through countless overly-aliased 3D maps on the Playstation One and this game really seemed like a breath of fresh air. I don't expect anyone to agree with me here, but it seemed like a game that really turned a corner for Nintendo (though it could easily be argued that we haven't really seen anything come of it).
Thanks for reminding me that, unless a monumental Wii Virtual Console announcement makes it redundant, I should set the system up again sometime soon.