In the Season Six episode "Sundown" Dogen tells Sayid how Jacob offered to return his son, who Dogen accidentally killed in a drunken driving accident, provided Dogen comes to the island to do this job - but he can never see his son again. Sayid says that Jacob drives a hard bargain, and Dogen replies that Sayid was probably offered a similar bargain.
Sayid's bargain was to kill Dogen (and thus allow the death of everyone remaining in the temple)apparently in return for seeing Nadia again. Both Jacob and his nemesis make similar offers - restoring the life of a loved one - in return for service.
I'd just about bet a kidney that we'll find out Jacob was responsible for engineering the death of Dogen's sone, just as he was responsible for Nadia's death. Although Dogen calls Jacob's nemesis "evil incarnate" I wonder if he'd still feel that way if he knew he'd been manipulated.
I think what this is all leading to is the question of completely free will, represented by Team Smokie, and life guided by a higher power, represented by Team Jacob.
I think this is the writer's attempt to tackle the "why does God allow bad things to happen" question. Think about it - if "everything happens for a reason" that means that some pretty horrible things are allowed to happen - in fact, designed to happen - to serve some greater purpose down the road. The Man of Faith has to trust that this greater purpose is worth the pain and suffering.
Jacob is looking for people of faith for candidates to protect the island, while his Nemesis just wants to home (whatever that is). Nemesis wants people who have lost their faith. Sawyer had completely given up, not even caring if Un-Locke was "the Ghost of Christmas Past" (best line ever, by the way). Sayid had also given up, telling Hurley he was beyond saving. It's the hopeless that Nemesis recruits.
Nemesis frequently tells people they are now free. I think he means free from Jacob's manipulation; free to exercise their own free will without Jacob's guiding hand.
So, is Nemesis evil because he is trying to thwart Jacob's plans (presumably leading to a greater good). Or does freeing Jacob's followers so they can truly make their own choices make him good?
Alternately, is Jacob evil because he has intruded in people's lives and manipulated them into choices that suit his purposes? Or does Jacob's ultimate goal justify the pain and suffering he's caused? Right now it's impossible to say, since the goal is unknown. Our final feelings about Jacob will probably be determined by what that goal is, and if we feel it's worth the cost.