Best
1. Zelda Ocarina of Time
2. Mario 64
3. San Francisco Rush 2049
4. F-Zero X
5. Wipeout 64
Honorable Mentions: Scores of games on this, my favorite console...
Worst
1. Dark Rift
2. War Gods
I have a good 150 N64 games, but the N64 doesn't have many bad games... though I do intentionally stay away from genres I would dislike like football or wrestling games (I will admit the the NFL Blitz games aren't too bad, but wrestling? Yeah, I really dislike any and all of those.). Those two fighting games there are really, REALLY bad, though. Some N64 3d fighting games are okay to good for their time (Mace: The Dark Age, Flying Dragon, Fighter's Destiny 1 and 2, Mortal Kombat 4, Dual Heroes, Bio Freaks), but those two... man are they terrible. Clayfighter 63 1/3 and Clayfighter Sculptor's Cut are masterpieces in comparison, and those two are pretty mediocre. Overall N64 fighting games have aged worse than the 3d platform-adventure games or the racing games, but at least some of them can still be some fun if you can still enjoy 5th gen 3d fighting games... but Dark Rift and War Gods? Only play if you like to suffer.
Also, Aidyn Chronicles is a legitimately very good game; if you can deal with the slow pace and horrible bugginess of the game, there's a huge game there with a lot to love. It definitely isn't for everyone, though, sure. I also like Carmageddon 64. Ignore the "it's the worst N64 game ever!" stuff. It isn't, at all. Sure, it's not the best, and it isn't as good as the original Carmageddon for the PC, but it is an okay game that I, at least, find fun to play. Oh, and Hybrid Heaven is a pretty decent game as well.
Yeah, the game has bugs, but there's so much there if you have patience... though yeah, backing up your save files somehow is a very good idea.
The N64 controller, painful to hold? What? I couldn't disagree more, it's quite comfortable, and certainly is vastly superior to anything from Sony... Sony's controllers are all far too small, and that dpad-above, analog stick-below design is terrible. It makes using the analog stick a bit uncomfortable, and the d-pad's no good either thanks to that awful missing center. And the analog sticks are RIDICULOUSLY inaccurate too, anything from Nintendo is better.I don't mind the N64 controller that much, but it doesn't sit in two hands as nicely as does a Dual Shock (recommended one-hand cradle grip = lolwut), and on top of that I have two remaining complaints: One, the stick in the middle does wear out (and I've never played any of the Party games, so it's just from normal use, more or less; it's definitely less durable than the Dual Shock, which isn't rock solid either, but much closer to the durability of a modern controller) with the plastic joystick wearing itself down into a chalk-like substance collecting around the middle ball; two, the thin top of the joystick is very uncomfortable to press sideways against, and it's easy to slip your grip otherwise. The PSX controller would have this problem as well but that, like the modern Xbox Joystick, gives you a well-shaped and well-textured middle nub to grib your thumb. Oh, and don't even get me started on trying to dash through levels in Mischief Makers using the buttons...argh. However, as mentioned the Hori joystick seems very nice, but also very small.
If you can overlook massive amounts of pain (either to the fingers or your eyes), there's a few good ones I didn't notice in people's lists:
I know I'm biased -- the N64 controller and Saturn 3D controller are probably still my two favorite gamepads ever, while the Playstation is a bad controller and I'm still sad that its design is now the basic layout of all controllers -- but yeah, the N64 controller's incredible, one of the best designs I've seen.