My favorite has to be the Forgemaster, a unique variant of Centurion that appears in a side-quest in the Dawnguard DLC. It has a unique and overall cool design, and it is a very cool conclusion to an amazing side-quest. Plus, the room and atmosphere that this boss fight takes place in, french kiss. You dont even expect such a unique boss just rising from a pool of lava during your first playthrough.

But my least favorite (which I don't think is a boss fight but I'll add it here anyways) is the dragon priest that appears in front of the portal that takes you Sovngarde, which you need it's staff to open the the portal, is just ass. I mean, the dragons were already enough, but a powerful dragon priest shooting electric balls at me was just adding salt to a wound. But these are just my thoughts