I'm with zombie84 in that I really liked Watto. He was probably one of the best parts of the trilogy for me.

A lot of scenes in the prequels are bittersweet for me, because I liked the ideas but was disappointed by the way they were done. For instance, I was really excited by the fact that Boba Fett was going to be an integral part of AotC, and that the Slave I would be in it and all that, but I was disappointed by the way it was actually done.

The colosseum scene in AotC was pretty awesome though, before the Jedi showed up anyway.

So here's a list of what comes to mind at the moment:

TPM: Watto, Darth Maul vs Obi Wan (the three-way fight was way too fancily-choreographed, but I remember everyone cheering in the theatre when that force field went down and Obi Wan just released the fury on Darth Maul)

AotC: the colosseum scene, the fact that Christopher Lee was in it

RotS: I honestly can't think of anything. I've only made it all the way through once