Any boss fight from Legend of Dragoon will make you cry yourself to sleep that night.
wut? Most aren't that hard. The only one I can particularly remember is Divine Dragon, which really just took forever. <_<
Most Kingdom Hearts bosses
Stallord, Aganarok, Zant, Ganondorf-Twilight Princess
Magus-Chrono Trigger-http://youtube.com/watch?v=s-sZ1f91ql4 (take note of the music; it's one of my favorite tracks in any game)
Kefka-Final Fantasy VI-http://www.youtube.com/watch?v=GG5ELlPZFGI
Ganondorf-Wind Waker-http://youtube.com/watch?v=H_yXb6rLHJg&mode=related&search=
Meta Ridley-Metroid Prime-http://youtube.com/watch?v=O5nnKUDHrvA
Bowser-Super Mario 64-http://youtube.com/watch?v=sNs0t3s87Es&mode=related&search=
Everything in Shadow of the Collosus
Mecha Sigma-Megaman X4-http://youtube.com/watch?v=JUiFVSES3QQ
Granfaloon-Castlevania: Symphony of the Night-http://youtube.com/watch?v=tShloCyMVlI
Computer Virus-Kirby Super Star-http://youtube.com/watch?v=epJXHs_N4_A&mode=related&search=
To name a few. >_>
Modify'd for videos.