Speaking of Zelda bosses, SS' Ancient Automaton: Koloktos (4th dungeon boss) has gotta be the best Zelda boss I've faced since the series made the transition to 3D. It's funny, cuz when I was fighting him, I had my moments of visible frustrations, but the moment I defeated him, I looked back at it and was all like, "that was...pretty ****ing awesome actually."
Psycho Mantis in MGS1
Sniper Wolf in MGS1
Vulcan Raven in MGS1
Metal Gear Rex (once i'd figured out how to kick his ass)
Yeah, pretty much every boss in MGS1. Some were good in 2.
The Colossi from Shadow of the Colossus.
Ra's in Arkham City.
Mister Freeze in Arkham City.
Reed from Splinter Cell Conviction (not so much for his power, but the way the scene played out).
T-90/Birkin in RE2.
Shao Kahn (just for what it felt like to put his ass down).
The shape-shifting panther in Devil May Cry.
Any boss in Onimusha.
Your choices are fine. So let's get that out of the way.
But...Freeze?! He walked at a slug's pace around a giant room, you could tab out to see the dozen or so ways to beat him, then sit around for however long waiting to ambush him in a slightly different way than last time. It was monotonous and not the least bit challenging.
I felt like it was a final exam for the tutorials each time you get a new move, except you got to look at your notes and had as long as you needed to complete the test.