I definitely have to say that D&D and JRPGs lead the way in terms of the weirdest monsters ever found in RPGs...heck JRPGs probably have D&D BEAT considering some bosses.
like the Great father.
All the characters in Persona 2: innocent sin have daddy issues, so of course the best thing for the villain to do to? SCREW WITH THEM!!! And "play as their fathers".
Definitely kind of unexpected, but I think I'd have been a little more afraid of his forms in Eternal Punishment.
Let's also not forget Tales of Legendia and Shadow Hearts. I was one attacked by a watermelon elemental and found another set of monsters that was a giant block and a pair of scissors. Now that's just random. XD
But shadow hearts just doesn't need words. Especially some monsters in the first game that hit you with VERY questionable appendages.