Maybe I'm a bit jadded but not too many titles from the current gen make it into my list of all-time favorite games. That being said, a few games have really blown me away.
Super Smash Bros. Melee: This Godzilla of a sequel is still my favorite GC title. It's like a tribute to one of the greatest companies in gaming. Tons of modes, tons of tropies to collect and an all-star cast of Nintendo characters. Last but not least, the Nintendo stars kick the crap outta each other for no story-driven reason. You gotta love it.
F-Zero GX: Slick GC visuals, a sweet pulse-pounding techno/rock soundtrack and some of the fastest furturisctic racing in the universe. Yes, it's tough but not impossible.
Virtua Fighter 4: Evolution: I missed out on the Virtua Fighter 2 craze in the arcades and on the Saturn. From what I've heard, VF4 was like the second coming of that great game. VF4 Evo was even better. It has amazingly deep gameplay and the Quest mode brings the arcade experience to your living room. It isn't newbie friendly but my fighting game improved dramactially when I started playing this game. And I heart Pai.