I just spent a while on Reddit reading this:
JarJar and the guy makes some very interesting points about his actions in The Phantom Menace, especially. His evidence is more laid out here, with pictures:
Article.
This is not a totally new idea; the guys at Robot Chicken thought about it before.
RC. JJB was apparently originally supposed to be a mercenary who betrayed Qui-Gon Jinn
Item 9, and, as pointed out by the article above, his actions can be seen in an evil light, if you get past the comic aspects of his character. And hey, he definitely has the eye color for it
Sith eyes. I have a feeling it is just a fan theory, but it would be amazing to find that he was somehow connected with the Emperor's plots in some way other than a just a well meaning buffoon to manipulate.