Ganon from OOT And LoZ
Shadow Link from AoL
Probably Perfect Dark Gaia phase 2 from Sonic Unleashed
The Dark Queen from Sonic & the Black Knight
Solaris Phase 2 from Sonic the Hedgehog(2006)
Red from Pokemon Gold/Silver
Wow, I have a list of these^^
Okay, so from OoT, I liked Bongo Bongo and Twinrova.
From TP, I liked Fyrus, Stallord, and Zant.
In Paper Mario, I liked Huff N. Puff and General Guy.
In The Thousand Year Door, Macho Grubba, Cortez, Doopliss, Gloomtail, Shadow Queen, and Bonetail.
And in Starfox Adventures, I liked Galdon, RedEye King, and Drakor.
I tend to like bosses that actually give me a challenge, or bosses that are fun.
When I have a boss battle, I want to have barely any life left when I finally kill them, and I want the battle to be EPIC.
If I have to be revived a few times, first, that's fine, too^^
But the easy battles just get too boring D:
I gotta go with Kaptain K. Rool from Donkey Kong Country 2: Diddy Kong's Quest. This was probably my all-time favorite game as a kid, and it took me FOREVER to reach him. Not to mention the atmosphere, music and fight itself was just awesome at the time.
But I give an honorable mention to all 16 Colossi in Shadow of the Colossus.