Hardest: I don't know why but I never seem to find bosses that difficult in video games. I enjoy them but generally I like it because you get to go all out on them and can use all the items you've obtained, etc, etc. That being said...
Gohma from The Legend of Zelda: The Wind Waker
Don't laugh. I remained decidedly spoiler free for The Wind Waker and hadn't seen any of the previews detailing how to beat this great big giant fire crab thing. It took me waaaay too long to work out the grappling hook on the tail thing and I spent a good few days running around trying to work out how the hell to attack the damn thing. Kind of the hardest for the wrong reason though so...
Shadow Queen from Paper Mario: The Thousand-Year Door
By gum, she's difficult... not only is she invincible for like the first half, and you've already just fought Bowser and Grodus in a row so chances are you're item-less, you have to defeat the 150HP monster about a million times before she really goes down. She's also frustrating as you go through the same 10-year long cutscene showing everyone in the game "wishing" for Mario a million times. And for a final exaggeration, it took me 4,815,162,342 attempts to defeat her.
Coolest Boss: Love or hate Twilight Princess, there's no denying that every boss in the entire game is 100% awesome. That plant dude bursting out of the swamp, that worm thing underwater, a dragon soaring through the sky, a kind yeti turning into this ice monster thing, a Zant revealing his true -- oh. Well every boss in Twilight Princess except Zant then.
Easiest Boss: Bowser. Super Mario Bros. No question.
