This is all my opinion and it's In no particular order:
1. Zelda: Majora's Mask:
Best Zelda game, the most creative, love the time travelling system and the story, maybe lacking on the dungeon department but still the sidequest and story are very good and interesting. And Song of Healing is the best Zelda track. Good game overall.
2. Mario Sunshine:
Best Mario game, I love the sense of exploration it gives and the good challenge. I really loved the twist of finding out Shadow Mario was Bowser Jr. I actually loved the FLUDD, the soundtrack and the levels.
3. No More Heroes:
Best beat em up/HacknSlash - As ED described it "this game is the internet on a disc" the story is so awesome and creative, an otaku buying a lighsaber off eBay? lolowut!? the gameplay albeit simple it's addicting and the bosses and soundtrack are amazing!
4. King of Fighters 98-02:
I really can't ever decide which is my favorite, but being the fighting game addict that I am and this being my favorite fighting series I'd say it's between those 4 because thats where the fighting really gets fast paced and it's just very great fighters.
5. GTA: San Andreas:
I love this game, best GTA hands down, the gangster storyline is very awesome and fitting for the GTA games and the RPG system they put on this game was very awesome. You eat too much and you become fat, you work out a lot and you become a bodybuilder, what other game does that!? The soundtrack was very good too.
5. Banjo Tooie:
My favorite Banjo game, too much to do and too much to collect, so much content, it was awesome. The soundtrack and bosses were very epic too.
6. Pokemon:
I can't ever decide which one is the best, they are all so beast. My favorites are Yellow, Crystal, Emerald, D/P and SoulSilver. I also love Stadium/colluseum/XD and Snap. Most of the side games are garbage though.
7. Conker's Bad Fur Day:
Hands down the funniest game ever.
8. Brutal Legend:
Second funniest game ever, and I love it because Im a metalhead lol
9. Smash Bros Mellee:
Best one of the three, the game is very balanced and very fun.
10. Can't decide, so I'll just put my honorable mentions and inser any of them here.
Honorable Mentions: Silent Hill(all) Sonic(most of them) Mario Kart Double Dash, Shawdow of the collusus, FF 1-13, Street Fighter II, the Vs. Capcom Series, Mortal Kombat 2, 3 deception, armageddon 9, Resident Evil 1-4, Castlevania games, Phoenix Wright, Kingdom Hearts, Metal Gear Solid, Dead or alive, soul caliber, Deadrising and Killer Isntinct. That is all.