I've seen a lot of theory about Jacob and MIB, with one being "good" and the other being "evil." There are definitely people who disagree, but the counter-arguments are scattered, so here's mine all in one place.
I think that the labels "good" and "evil" can only really be applied to people's actions, not the people themselves. One very common theme throughout Lost is that people have both "good" and "evil" qualities. Mr. Eko was a notorious drug smuggler in Nigeria, but at the same time he still wanted to protect Yemi. Even though he was working to provide for Sun, Jin did some evil things in his work for Mr. Paik. Kate killed her stepfather to save her Mother from his abuse, but that doesn't change the fact that she still killed a man, no matter what her motivations were. Before Season 6, Ben was arguably the most "evil" character in the show, but he was repeatedly shown to have a good side, even if it didn't manifest itself that much. But do these actions that mean Jin, Eko, Kate, and Ben are intrinsically "evil"?
Now when it comes to Jacob and MIB, things appear to be more clear-cut. Jacob helps people, and MIB uses them. But we have been repeatedly shown that both Jacob and MIB will manipulate people for their own ends. The difference comes in the way that they do so. This was exemplified in Ab Aeterno, although it definitely came up before. Jacob accrues favours by offering to help people, or to give them a gift (which he delivers). This trait is what anthropologists call a "Big Man"; by offering someone a gift or help (such as Richard's immortality), Jacob causes a debt, so he can call in a favour down the road when he needs one. In Ab Aeterno, we (probably) see Jacob making Richard immortal, but Richard isn't asked to do anything immediate in repayment.
On the other hand, MIB asks for someone's help, promising a usually fabulous reward in the future. When MIB firsts reaches out to Richard in the hold of the Black Rock, he first asks for Richard's complete compliance with his request without telling him what it is, and then offers to "eventually" reunite him with Isabella. He did this with Claire and Aaron, with Sawyer and getting off the island, and he might do it with Jin and Sun (although Jin doesn't really appear to be "under his power").
Because of this, Jacob is seen more often to be helping people, and MIB is seen to be using them (as I said above). Based on our value system, we jump to the conclusion that Jacob is "good," and that MIB is "bad," even though we don't really know or understand their motivations: we're just labeling their actions. Once we DO know and understand both Jacob's and MIB's motivations for their actions, THEN we can judge them properly and rationally.
So I guess the moral is, don't be too hasty to label people as "good" and "evil," especially not Jacob or MIB. There's a lot more to the story that we don't know yet.