Think in the end, Lost will be like real life, no real answers (in this world, at least) to a lot of the mysteries, but here goes some theories.

I agree with a couple of the above, Smoke Monster was created from MIB being sent into the light cave by Jacob. Thus, although Jacob's brother's BODY is empty, his soul/spirit/whatever you want to call it, is inside Smokie. Therefore, it really is Jacob and his brother still having their "contest" over time.

Jacob has, over history, drawn people to the island to find a replacement, just as his "mother" did before him (and she alludes to someone prior to her too). The MIB actually questioned him about this long ago, suggesting that they will always "disappoint" Jacob or some such. Jacob's only way off the island is to be replaced, just like his adoptive mother. (which is why, once she has a replacement, she thanks her other son for killing her, she can leave now). So he brings people there as candidates to see if they are "pure" enough to not want to use the island's power for anything and simply to protect it. We can see that many that he brought are not pure, that they want to use the power, from the Dharma Initiative to Charles Widmore to the owner of the Black Rock. Now, we might not call that "evil", just scientific curiosity, but if, by trying to exploit the power, humanity would destroy the whole world, then even if the intent is not evil, the actions might lead to a great evil.

So, does Jacob do "bad" things occasionally to protect the source? That's conceivable, though, again his theory seems to be that humans should be allowed free choice and so, although, he appears to often manipulate them to the island, he lets them make their choices after getting there (so far, he has yet to find a candidate who will "choose" as he did, to protect the source, although the Real Locke seemed pretty close to this in his belief system)

The MIB's motivation is what he said as a kid, he wants to LEAVE. Jacob prevented him leaving like everyone else can leave the island, by dying, by forcing him to transform into the Smoke Monster and "killing" his mortal body. Now, he appears tied to the island. Somehow, he apparently has it in his mind that if all the candidates are dead and Jacob is not replaced, then he can leave (mayb if the rest of the Source leaves, He can too??). In this way, he may actually be "rooting" for Charles Widmore to succeed. If Widmore finds a way to tap the energy source, maybe he can finally get off the island? I am totally guessing here.

As for the dead people appearing when they are not the Smoke Monster/MIB imitating people, I think maybe the Light Source is the where souls go when they die and, so on the island, maybe a soul can occasionally get out of the cave and speak to people on occasion. This would explain Claudia's ghost. These ghosts wouldn't necessarily be good or evil in intent. I don't know that being dead makes them any wiser than they were when they were alive, and their motivations wouldn't have to be much different than when they were alive. Thus, Claudia's ghost may not have intended to send her 2nd born on a path of evil, she may have simply wanted him to know his own people or exact a little revenge on the woman who killed her and supplanted her.

Talked a lot. Lots of guessing. My guess is that, in the end, the answers to this show are what you want them to be. Just like religion in real life.