Personally, I'd have to go with the fight with Bowser in Luigi's Mansion. It was a huge surprise, and a fight with a non-Mario plumber vs. Bowser is just too cool not to mention.
"Only I have the brains to rule Lylat!"Most epic is easily ANDROSS in starfox 64.
YOU'LL NEVER DEFEAT ANDROSSSSSSSSSSSs
oh man, awesome, awesome choice. miguel is definitely my favourite boss. it was so emotional, and the battle itself was so... forced, but so necessary. and he was also hard as shit! weakmindedminded > turn black > holydrgswd in a single turn will kill you, without question. a blade of energy emanating from an old man's hand? damn right he's awesome.Staying in the Chrono series as far as plot goes I think Miguel in Chrono Crossis my #1 favorite boss fight... it makes me sadface to think about it but the plot right before him leading into a battle that neither side really wanted to be in was really good, the music made it better and the fact Miguel had some cool attacks like HolyDrgSwd or however it was abbreviated made it a really great boss fight.