Tyler Glaiel

It's this game

http://www.newgrounds.com/portal/view/439647

I'm pretty sure I'm not alone in saying this, but beating Draygon through electrocution was probably the greatest way to fell a boss in any game I've ever played, and even though he's really easy to beat that way I still look forward to that fight every time I replay Super Metroid.

Besides that, the Nightmare in Metroid Fusion is one of the creepiest bosses I've ever faces. The way it's face melts is just horrifying, and you almost feel sorry for it because you can tell it doesn't enjoy being alive (it was engineered as a biomechanical creature, after all, so it's some horrible frankenstein's monster of sorts), and the build up to that fight is just perfect.