I think virtually all boss battles, if not, at least nearly all final boss battles, are weird. I mean, these guys are supposed to grab your attention and stand out from normal baddies. Also, it requires you to use all the skills you've learned so far.
That being said, I COULD just say "Anything from a Mario RPG", but I'll elaborate a tad:
Bowyer: Looks like a bow, talks like Gollum crossed with Yoda, breaks the 4th wall with a set of SNES buttons in front of him that disable moves.
Those bosses in Smithy's place: What was it... Clockwork, Domino, Hoodie, or something... yeah, just go back there sometime and see what I mean.
MukuMuku: Does this count? He's a cloud of gas with two different names that's always following you around.