Hardest NPC I can think of right now, is probably The Deposed King from Darksiders II, when I was trying to fight him around level 13 (or something like that).
He was just too difficult, had to wait and level up and come back later.
Also Gorewood from the same game was pretty hard... And Bheithir.
Pretty much all the bosses from that one quest were a pain in the butt. >_>
Oh, and the Egg Viper from Sonic Adventure 1... When it does it's wild "take out the platform you're on" thing once you kill it, and you have to dodge... So freaking difficult to time that right.
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