Super Mario 64
Kirby Super Star
Shadow of the Colossus
No More Heroes
Might & Magic: Clash of Heroes
Super Punch Out!
The Legend of Zelda: Majora's Mask
Star Fox 64
Final Fantasy VI
Wild Arms: Alter Code F
3D Mario game that is. Let's not talk about Sunshine (It's not bad, just clearly not the best) and focus on 64 and the Galaxies.
Super Mario Galaxy may be the single best reviewed game of this generation, and I completely understand it. It looks beautiful, it sounds beautiful, it plays beautifully, and it's great fun. Great game. It also helped that it was majorly influenced by Super Mario Bros. 3, widely considered to be the best 2D Mario game. A good source of inspiration for sure. While I'll take all the airships I can get, this is where Galaxy's major flaw comes from.
Level design in Super Mario 64 and Super Mario Galaxy are totally different beasts. In Super Mario Galaxy, you pick a galaxy, pick a star, and are then thrust into a very specific location depending on which star you chose. From then on the courses are very linear. There might be a secret star in addition to the one you chose, but most likely you're just going to run and complete objectives until you eventually get the star.
That is unfortunately very different from a huge part of what made Super Mario 64 so great and innovative. You started off at the castle, already a huge playground, and then made your way into the painting. Sure you would select a star before you went into a level, but it very rarely mattered. You could get pretty much any other star in the level no problem. Levels were huge sandboxes of different places to explore and different things to try. Did anyone run straight to King Bob-Omb their first time? No, they jumped on platforms, rode koopa shells, got shot out of cannons, and just generally did whatever they wanted. I was having sandbox fun long before Grand Theft Auto.
My hopes are low that Galaxy 2 will surpass 64. They've gotten rid of the hub world from Galaxy, because they thought it was boring. If only instead they'd looked back to 64's and realized how just great it could be. It also doesn't appear that there will be any major level design change. I guess I'll have to wait until next generation to get a game that might be better than Super Mario 64.