Jango Fett vs. Obi-Wan.
The overall story concept.
Battle droids (until they started talking).
The design of the clones.
Most of the Republic equipment, actually.
Naboo. Just seems like a neat city to walk around in.
Coruscant. The entire planet is one big city.
I'm sure there are a few other things, as well.
I, in general, like the prequels as well. But I like them in the same way that I liked games like Star Wars: Galaxies or Knights of the Old Republic II in that the idea is fundamentally sound, and a few things were executed pretty well, but overall they just weren't fully realized and poorly executed and suffered because of it. Which is sad, because they all could have been pretty awesome.