I haven't mulled over this question in a while. It's hard to pick one, though...
Sonic 2 is the best 2D Platformer there ever was. It blends great art style and a fantastic soundtrack with blazingly fast gameplay. Sonic 2 has the perfect balance between carefully crafted, obstacle-ridden levels and the loops and springs that send Sonic into overdrive. The zones branch in more directions than Sonic 1, but they're not labrythine messes like in Sonic 3 & Knuckles. Oh yeah, and this game has the best bonus levels of any Sonic (OMG 3D!). Seriously, it's never been done any better. And it never will.
Mario 64 is the best 3D platformer there ever was. Nintendo hit a home run their first time out, and no one's gotten particularly close since. Mario 64 is deep, varied, and versatile. I swam, I flew, I raced penguins! It's one of the milestones of gaming history, the most important 3D game ever. It's not the stunning visual showcase it was in 1996, but it's still fluid and fun. I've never seen a more brilliaint reimagining of a franchise.
As far as the whole package goes, Zelda: Ocarina of Time is probably the best game there ever was. It has the visual flair, the cinematic presentation, and the tight gameplay that really took Zelda and Nintendo to a whole different level. I don't think I've ever played a more balanced game. It's something that I can't look back on and say, "It was great, but it would have been better if they fixed such and such." The closest thing to a flawless game we're bound to ever see.
Metroid Prime might be the most immersive game there ever was. I think last time I made one of these lists (around November 2002, heh) Prime might have been my number 1. Looking back on the game, it's obvious I've played a few better, but this was still a really great showpiece. The game sucks the player in like nothing else I've ever experienced, mostly with its lavish attention to detail. Tallon IV is a world, a reality unto itself. The Prime gameplay is solid, but I think it will really be remembered for the unparalleled experience it creates with its incredible artistic visuals.
Zelda: Wind Waker has the best presentation ever. Everything about this game just clicks from a visual level. I wasn't a true believer in Celda beforehand, but when I popped this into my Cube and saw Outset Island in its Saturday-morning-cartoon glory, I was floored. This is Zelda through the eyes of a little boy. The monster designs were especially awesome (my favorites were the ReDeads and the moblins). And the plot, while simple, was presented with such eloquence and beauty that it seemed downright un-Nintendo (OoT tried, but it was nowhere close to this level). Also, sunken Hyrule was pure magic. This game had a lot of flaws gameplay-wise, a lot more than your average Zelda, but I find myself getting past them and longing to back through the game once more. Artistic brilliance.
Resident Evil 4 is probably the coolest, most visceral game ever. It really feels like a Hollywood production that you're in control of. RE4 is the game of the generation for me because it starts with an incredibly frantic, heart-pumping sequence (the village scene), then proceeds to continually top itself for the next 20 hours or so. The game is like 20 or so insane set pieces strung together to create the best action game ever. I think this might be the only game that I immediately started over the moment I was done with it. I've beaten it three, maybe four times as of now. RE4 is the Ocarina of Time of this generation; it brings EVERYTHING together to create an irresistible, nearly flawless package.
Going through my list, which I guess I did chronologically, I notice that the gaming medium has really changed since it went 3D. The best games today are really about more than just gameplay. It's about how the gameplay, visuals, sound, presentation, and all the rest meld into a final product. I think games have evolved into more of an experience (artistic experience?) than just mashing buttons to move an on-screen avatar to save the princess. It's exciting to think about where we'll go next.
