My favourite boss... That's actually rather challenging. I'd say it would have to be something from The Legend of Zelda series, but what exactly I do not know. As Mr.Man said Molgera is a pretty awesome boss, with great music and a lot of fun.
Twilight Princess had some awesome boss battles, if not them being the best part of the game, with Stallord coming to mind.
Onox from Oracle of Seasons was challenging and a lot of fun, particularly at the end.
And finally Puppet Ganon, despite how much I despise it because of the snake form, is one of the best final bosses I have ever fought. Amazing music, combined with a wide variety of necessary attacks and a real challenge. Yeah, probably Puppet Ganon.
The correct answer to this is CLEARLY Hiroyasu Kurahashi & Shinya Akiba from Killer7. I mean for the love of god, they're old Japanese men wearing suits with their heads mostly blown off. AND THEY THROW BRAINS AT YOU.
- Spongebob Squarepants Battle for Bikini Bottom:
The last boss is in two sections, the first were you fight a massive karatea spongebob robot which was actully kinda hard. The my favourite bit, you go inside the robot and have to make it around destroying parts of it, while avoiding a certain robot individual.
Also the music was epic.
- NSMB Wii
The last boss, Dont want to spoil it for those who havent played...
EDIT: Finally I can say Ive level'd up and some cheesey jo...Stop Its hammer time!
Thardus from Prime 1 is one of my favourite bosses, I just like his concept a lot.
Gleerok from the Minish Cap is pretty awesome too.
Uhmm... Who else....
Oh right! Albus from OoE of course, the battle and music are both awesome. And, because I have to add a Touhou boss, I guess Mokou, because I like her attacks and she's the only extra boss I have beaten (I actually beat her for the first time just yesterday! Woo!(Not the spellcard ))
Oh, and Magus should be mentioned too. You know why, I don't need to tell you.
Shadow Queen from Paper Mario: TTYD. I don't know why, but I just really like that fight.
There's also, of course, Crystal King from Paper Mario 1. Obvious reason is for the music, but the battle itself is pretty fun as well. I also really like the final Bowser battle in PM for the same reasons.