Devil May Cry 3's final boss is the best I've played. It nails the atmosphere and the setting, the opponent is a natural one for the game to end on, the fight is a culmination of everything good about the game, it's tough without being cheap, it's incredibly fast and frenetic. It's also is a great final boss in an action game, which I think are much rarer than great final bosses in RPGs (I think the only RPG I'm a big fan that doesn't have a great final fight is FFIX, whereas there's not many action games I like that I'd say have one). The only challenge I can think of to DMC3 is MGS3. I'd say it wins on setting/atmosphere - both visuals and sound are superb, and the scenario is more than worthwhile - but while it's a solid fight, it's not as special - too formulaic.
Bosses in platformers I often find to be weird. Not necessarily bad, but just strange. The enemy will inevitably have an incredible volley of attacks to throw out in order, followed by it waiting for you to hit it!
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Praise the Black Turtle, Game of the Decade Guru Champ.
(Well, I never promised creativity, did I?!)