Flowering cactoid caused me a lot of trouble, probably one of the hardest marks in the game (at the beginning of the game, when you've only got vaan, and you're not overleveled, he's awful.)
Antlion, made me hate bugs

he was the first boss i couldn't kill with quickening combo's...
Elder Wyrm was painful too, but he only took me about three tries.
I killed both Demon Walls with quickening combo's