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Hitman's "Final Bossfight" will always be in my mind 
I killed them both in one move... with one bomb and that was it...
Also No More Heros' final boss fight (the true ending) was just mentally cool and full of plot twists and random shizzle to fry any brain.
OH OH! Also Shadow Of The Colossus' final boss fight was a bastard...but well worth the effort |
Shadow Of The Colssus final boss battle is very easy once you figure out your not trying to attack the thing head on.
....Or maybe I'm just so used to battling the guy I forgot how hard he can be the first time
Final Fantasy X's final boss fight can be a bit hard if you didn't give Kamari doom and such.