Here's mine, in order from best to worst:

Ganondorf (of course!)
Zant
Ghirahim/Veran (Can't decide!)
Ganon

Majora's Mask/Skull Kid
Vaati (Mage)
Vaati (Eye)
Nightmare Ganon (Not sure if that's his name, or if he actually counts)
Agahnim

Dark/Shadow Link (Zelda II)
Malladus
General Onox
Demise
Bellum

I left a space because the top section I really adore, the middle are okay, and the lower ones are bad designs in my opinion.

I never mentioned the Wind Fish - I don't actually know if he's a boss fight or not as I've never managed to finish Link's Awakening! But if he is the last boss of the GB version, then I guess I'd probably put him in the bottom section as from what I have seen of him, I don't like very much.

What about you guys?

Edit: Let me know if I missed any main ones. And I'm just taking into account the end of game bosses, or ones that had a significant role in the main plot. Not the end of dungeon bosses.