It's a little obscure, but some of the funnest boss fights I can remember were from "Mischief Makers" on the N64. Also, there was a level in one of the TMNT games where you had to toss Foot Soldiers towards the screen to defeat the boss- that was pretty innovative.
There is only one best, though... Psycho Mantis, from MGS. (I... can't read your mind!?!?)
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Killing that robot makes me want to go home.
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