My picks would be
Super Mario 64--I've only played it on the DS which sours the experience a bit, but to be honest, the level design isn't all that great, and the gameplay is a bit...eh. The camera is something pretty horrid too.
FFVII--Worst PS1/2 era FF. Yes, that includes FFX-2.
Zelda: Majora's Mask--Loved OoT, hated this with a passion. Imposing a time limit on players and essentially deleting their progress every 72 game hours was a killer for me.
Halo--Terrible level design, very repetitive. Multi-player, while interesting, is ridiculously unbalanced and cheap. One ironic thing: the level everyone said was the worst and most repetetive was the only level I actually liked--the Library. Go figure.
Super Mario World 2: Yoshi's Island--I owned this back when it first came out, never understood why everyone loved it so much. I beat it, sure, but for me it was pretty boring. And Baby Mario was a prick.
Deus Ex--Simply brilliant. The best story I've ever seen in a video game bar none, excellent and varied gameplay, and to boot, an excellent fusion of game elements (RPG/FPS/Adventure). Over-looked by nearly all, game developers should study this game for ideas. No other game since released has touched this. Best game ever, in my humble opinion.
Banjo Kazooie--Some call it a collect-a-thon, but I wouldn't consider it one any more than Super Mario 64. And this has better level design, better graphics, more variety, a better hub world, a better camera, and in my opinion much better characters. I went back and played through the whole thing about year back, and it was just as sweet as when I picked it up way back in '98. Top five, definately.
Harvest Moon 64/Series--Unique, and not for everyone, but a great experience if it happens to be your cup of tea. Most game mags give it mediocre reviews, but I love it. Definately one of my top ten games of all time, no doubt.