I never really got enough Hero Factory sets to have a top 10, but here are some honorable mentions:
Evo 2.0 - a simple guy, but I guess I just love the color scheme. The only 2.0 set I got, but definitely my favorite.
Rotor - never actually got this guy, but he's probably my favorite of the 1.0 villains. Maybe something to do with the orange and the giant whirling propeller of death on his back.
XT4 - I never got any Breakout sets, which is a shame, because it was my favorite line. One of my favorite builds from would have to be XT4. I like how unique it was, and yellow is always a good thing for me. I only wish it would've gotten more attention in the story.