jechts final summon was pretty bad ass. i also enjoyed the japanese rock playing in the background.
the final boss from bionic commando on the nes was cool, i believe it was the first video game character to swear.
Nemesis was great for his imposing presence. I remember playing re3 and was always nervous that nemesis was just around the corner.
the boss in doom64 was sweet too
The Resident Evils have some of my favorite bosses like Tyrant from pt.2, Nemesis from pt. 3, and there are multiple cool looking (and hard to beat) bosses from pt.4 like the "El Gigante", Ramone Salazar after he mutates, and Lord Sadler at the end. Other notable game bosses are Ganondorf from Legend of Zelda, Sephiroth from FF7, and the Metroid Prime.
Jack Kruser from RE4. Their was that cool little knife fight then that little part where you have small battles then the big one when you have like 3 minutes to kill him. And Sephiroth. He was just so cool, confused, insane plus him killing Aeris pissed me off so the final battle made it all sweet. I mean I had Aeris as my top 3!!