I like each boss for their own reasons.

Queen: She's interesting because she's the only boss where there's more strategy involved than "dodge attacks and reduce life meter to zero" to defeat her.

Tuf Boss: This guy is easy and pathetic. However, stick him in the walls during a boss battle where you can't hit him for a nice surprise to an unsuspecting player.

Superbot: I just like this guy for the fact you can have Devan actually appear when you're not fighting him.

Uterus: Again, there's a bit of strategy involved in this fight in that you must destroy his the eggs that orbit him before he can be damaged. Also, his death sequence is somewhat unique, which is nice.

Bolly: This one is a blatant ripoff of Dr. Eggman's Eggmobile from the Sonic series (in particular Sonic 3). However, that's what I like about him. He's also a decent "robot" or "mechanical" boss and ideal for Tubelectric levels. But why on Earth did CliffyB place this guy in the Medivo levels?

Bubba: Okay, I'm not a big fan of this guy mainly because he's just not that interesting. However, he's alright as a "filler" boss; a boss for a middle of the game area where there's nobody better to have the player fight.

Bilsy: This is what all the bosses should have been like: his teleporting and homing fireballs are unique, and he can actually do more than one hearts damage to you in a single attack. I also like how there's more to dodging his attack than "jump out of the way". This guy seriously should've been used in the normal game.

Devan: This guy is an appropriate final boss, with the cliche "turn into a second form when life reaches zero" thing going on. No real complaints about him, except for the whole stomping glitch and the fact that he's pretty easy once you get the hang of him.

All in all, to answer the question, I suppose I'd have to pick Bilsy as my favourite.