All of the bosses from:
- Metal Gear Solid (each is completely different and imaginative)
- Metal Gear Solid 3 (same as above)
- God of War (the sheer scale of boss battles, and the "mini-games" where you have to press the correct buttons)
- Resident Evil 4 (mainly the battles with Krauser)
- Shadow of the Colossus (sheer cinematic beauty)
I don't rate boss battles by how cool the boss is (or looks), but by what you have to do to actually beat them (which is why I don't believe DMC3's boss battles were anything special). It's the boss battles where they make the act of battling them fun or imaginative that get my vote.
I also rate them by variaty of attacks. More attacks, better rating.