You know, after watching the latest web doc for Episode III, I think one of the characters from the prequels that I really enjoy is Obi-Wan Kenobi. I really think that Ewan McGregor was an excellent casting choice for that role, and he has made Obi-Wan one of my favorite characters overall.
As far as other characters, I tend to favor ones that appeared in the OT as well (Obi-Wan, Yoda, droids, soon to be Chewbacca), but there are also some cool original characters in the PT as well. Many of the Jedi (Plo Koon, Kit Fisto) as well as Padme, Dooku, Jango, and the Episode III baddie (I'll leave the name out here, just in case) are all neat as well.