I am having a lot of trouble thinking of any examples. My favourite game endings are the ones which go against the traditional boss ending actually, such as Halo or GTA:SA. If I had to choose, I would say:
1:
Barrett,
Psi Ops: The Mindgate ConspiracyIt's been a long time since I played the game, but basically I just remembered him as being pretty cool. His telekinesis was much more powerful than yours so you had to run around dodging train cars while you threw crates at him.
2:
Mad Jack,
Donkey Kong 64It has probably been well over a decade since I played this game, but Mad Jack is the only boss I remember fighting more than once just because I found it fun, not simply to progress further in the game.
3:
Mister Freeze,
Batman: Arkham CityBatman ends up locked in a room with Mister Freeze, who's had the cryogenically frozen body of his wife stolen from him. Convinced that Batman isn't intending to help, he attacks, and you have to incapacitate him while confined to one area. Unlike all of the other bosses you fight, he has various countermeasures for Batman's tricks and will update his tactics every time you land an attack on him, rendering said attack impossible. You have to use every technique available to you to take him down.
4:
Zuan Lun Wang (Shai Gen Kingpin),
CrackdownBasically this guy lives in the most hardcore, crime infested part of the city, in the tallest skyscraper in that area, which is filled with the most difficult to fight of all of the enemies of the game. And you have to fight your way through every level of it to reach him. If you have a deathwish, you could go there and try to kill him as soon as you start the game which is an interesting touch. You probably won't get very far though.
5:
The Nihilanth,
Half-LifeIt is at the end of Half-Life.