Ruby from FF7 is probably the hardest boss fight I've ever had.
I don't really have a top 10 though as most bosses in games aren't that difficult, in fact during games (other than RPG games) I tend to find the harder moments of the game being certain areas with waves of enemies, rather than the one on one boss fights.
“Anna, my strong, terrifying Anna.” -Cas
"You lack the requisite spine and testicular fortitude to study under me" -Elodin
Video Game GIF Thread