In terms of the strongest thing actually in-game... er, the rats at the start of the Morrowind Fighters Guild quest line. I had to go and sulk for a month after encountering them.
Chakravartin from Asura's Wrath attacks by throwing planets at you like bullet hell projectiles, and that's basically the weakest form you fight him in.
The 27 True Runes. The entire plot of every Suikoden game happens under their subtle guidance. You don't play them; they play you!
Max Payne because he can take infinite amounts of pain killers and not give a crap.