From Spyro 2, Ripto's Arena. That has a wholly new flashiness to it! And 3 stages!
From Spyro 3, Scorch's pit. Cool weapons, awesome boss, great music and he summons Buzz. Holy mother of god Scorch was the "Monster to end all monsters".
Not so much the battle, but the Boss Dingodile from Crash Bandicoot 3 is just such a cool guy....
From TS3, Princess is pretty awesome, but this time it's purely aesthetic.
The Feeble from Croc: Legend of the Gobbos. Why something so simple (and, to be honest, bad.) sticks with me so well, I'll never know. Maybe it's just that bland, yet powerful music that plays while you fight him? I think it's nostalgia.
Oh, and how could I forget the Rainbow Butterfly from Dark Chronicle? Every playthrough I look forward to that boss in particular. So nice to look at, great music, insane arena (A giant, gooey flower? Seriously wtf) and, most importantly, dynamic.