I don't think G-man is evil nessarily. I think he's more a middle man, he's certainly not on the side of the Combine, and is more interested in helping Gordon, or at least it came off that way in Eps 2 when he was talking about having to abide by certain restrictions. But, he's pritty pissed Gordon escaped him, Eli is G-mans revenge or "payment" for that escape.
I agree with alot of people here, I think he's a intergalactic mercenary, selling people to the highest bidder. I remember Breen saying he might "buy" Gordon from G-man for the combine, oviously he was kill before he could make his offer. But this brings up the question...who was employing Gordon to work for the rebels?
(Crist, someone needs to put up a spoilers warning)