I think Jacob is (was) the good guy, along with Ilana and her merry band.
Jacob's rival (in the form of Locke, but maybe he can change form, and maybe it was actually he who took the form of Ben's daughter and told Ben to follow Locke, Hell, maybe he is the smoke monster, and can just take the form of dead people) is the bad guy.
I don't think we yet understand the true significance of the original Losties. It's clear that Jacob brought them to the island, but none of them seem to know their purpose, and they have conflicting ideals.
Another thing that just popped into my head - Libby. She was on the island, and killed there, but she was also in the same mental hospital as Hurley, and she gave Desmond his boat (the Elizabeth). That's one thing they haven't explained yet.
Also, what about Claire and Christian, and what is there relationship to Jacob? Maybe they're allied with Jacob's rival, and they're evil.
Damn you, Lost!