In Metal Gear Rising: Revengeance, there are quite a few memorable boss fights that I often go back and play the whole level again just to experience once more. Metal Gear RAY (UG), Sundowner, and of course, Senator Armstrong. Monsoon can screw right off though, doing that fight without taking damage was an absolute *****.
Banjo-Kazooie had that climactic final battle against Gruntilda at the top of her tower, and with the music playing the way it was, it really made the moment seem awesome. You had gone through all of her shit after so many hours and final had the chance to take her down once and for all. I may be a bit biased with Banjo-Kazooie, but screw it, it's still one of my favorite boss fights. Most of the stage bosses in Banjo-Tooie are incredible in their own right, as well.
Call me out on this last one if you like, but I felt that the Human-Reaper in Mass Effect 2 was a really fun boss fight. When you get right down to it, you are basically fighting a giant Terminator that shoots laser beams. With handguns. Couple that with the music that was playing throughout the suicide mission, and you have one of the most memorable experiences out of the entire franchise. I loved it.
I'm sure I could think of more, but these are what I came up with off the top of my head.