I'd have to say Twilit Aquatic Morpheel. So much of the oceans are still unexplored, there is something inherently scary/creepy about potential deep sea creatures that we haven't discovered yet. Add in myths and legends of sea monsters and such and you have a pretty scary boss that is grounded in at least some plausible reality. There may very well be sea monsters like Morpheel in the depths of the sea, which makes that boss a lot more interesting (to me at least)
Also in terms of just aesthetic design it creeped me out. Maybe it's my aversion to tentacles & slimy things.