My favourite regular enemy got to be THIS GUY.
And speaking about bosses, I didn't encounter a lot so far, but I'm currently playing through the Mario RPG's and I guess I will come across a few on the way.
I liked Huff 'N' Puff from Paper Mario since he provided quite a challenge to me.
Also, Bowser Jr. has always been my favorite baddie. Fawful sounds pretty funny, too.