Ah, BlueFire's one was really cool. But (like all TP bosses) way too easy.
A boss (fight) in Zelda has to be hard, mean & scary, has to include enough sword fighting and especially smart use of items. I can't really pinpoint one. Oh, I hardly remember any TP bosses... I need to replay it.
Edit: When I asked my brother, he instantly said Majora's Mask, final boss. Or Shadow Link, OoT.
I had to think of Ganodorf in Ocarina of Time, epic battle which seemed to be without end.
Nobody mentioned a 2D boss fight yet...