I haven't played the N64 version, but Mega Man Legends (aka Mega Man 64) is an absolutely spectacular game. The voice work is phenomenal, and it's one of the funniest games I've ever played. The gameplay is fun, the exploration is fun, the music and sound works fine, the graphics are... serviceable, though I will say it certainly does better than any game of the era when it comes to facial expressions. The final boss fight is excellent, what with a) the background remix being a remix of Bach's Little Fugue for the organ b) a throwback to the Sigma battle in Mega Man X1, the greatest Mega Man game of all time (then Mega Man 2, then Mega Man 3, then Mega Man Legends) and c) "Are yo-ou ready?". Wonderful, wonderful game, and I'm surprised to see a bit of hate on it in this thread.
Aside from that, I can vouch that Zelda: Ocarina's constant praise is totally warranted, though I'll take Link to the Past anyday.
Mario 64 is great of course, though I actually preferred Mario Galaxy. And of course Mario World and Yoshi's Island beat it any day of the week.
Starfox 64 is frigging amazing. The only game here who's Super Nintendo prequel (though underrated) is inferior.
Uhhh... Yeah. I never really got into N64 that much. I mostly just played my Super Nintendo through that era. It doesn't help that it has ZERO Metroid, which is UNACCEPTABLE for a Nintendo console.
But yeah, mostly just the stuff others have been mentioning with noticeable praise for Mega Man 64, the underrated, under-hyped, MASTERPIECE of a game. Yep. Capcom sure can take Mega Man into 3D with no problems whatsoever. Yep. No crappy 3D Mega Man games to speak of, especially released on the PS2 with a 7 on the end.
