I'd have to say the Bouldergeist comet challenge was the hardest thing, boss-wise.
Baron Burr was really easy because they give you a 1-Up on one side and a Life Shroom (what's it called in Galaxy again?) on the other. Even if you opt to not get them just to challenge yourself... well, it's still pretty easy.
I'd like a boss battle that ****es me off and that has me looking at the screen after restarting the level saying "...aight, this time I'm gonna get this motha/b****."