Personally the final one in Knack.
First one to come to mind is Koloktos from Skyward Sword. There's definitely a lot of other good ones though, and maybe I'm forgetting one that I find more memorable.
lavos, chrono trigger!
edit: or Jowy from suikoden 2... but I'm not sure if that counts as a boss battle...
the final bowser in super mario 64!
Sonic 3 + Sonic and Knuckles ending with all Chaos Emeralds.
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Metriid Prime. No contest.
Penance in Final Fantasy X