Who is right, and who is good in the battle for the island? Anyone?
What we know: There are either two or three (Jacob, MIB, Widmore) sides doing battle now. They have gone to such lengths to convince us that Jacob is good, and that the MIB's plot must be prevented, that to pull a switcheroo twist on us now would be as close to unfair as could be.

Why "God help us all" if the O6 plus Ben plus Locke don't all get back to the island? For that matter, why do folks like Hawking even let Benjamin Linus go along for this trip? Why is it essential that he be part of the group that returns? He wasn't on the plane the first time, and it is assumed that exiled leaders are not allowed to return.
What we know: There is indeed something major at stake about the island if the cork metaphor is true. And the candidates did indeed have to go back so one could become the new Jacob.
What we don't know: Why Ben came back, or was needed to come back, or allowed to come back. Other than that he's quite possibly the coolest character on the show of course.

Did Ben know he'd need the Hyrda Island runway one day? Was it him who had it built, or was it someone else (Jacob, Richard)? Whoever commissioned it, how did they know it would be needed?
What we know: The runway allowed Lapidus to safely land with Ben, Sun, Ilana's group, Locke's body, and himself.
What we don't know: Whether the runway will also be used for 316 to take off, or whom it most benefitted: Ben, who got to return; Jacob, who got his candidate Sun and his protectors Ilana & Co. to the island; MIB, who got Locke's body.

Did the bomb work as they hoped, or didn't it? If it did, how will the show go on? Will the characters know each other?
What we know: There is an alternate version of 2004 in which the island is underwater, and the characters don't know each other, but have vague deja-vu's of recognition and remembrance. For the most part, their lives seem to be better. Juliet told Sawyer, "It worked" as she was dying.
What we don't know: How this is all going to resolve.

UNANSWERED (But I'm Expecting an Answer)

How did Jack get into the bamboo forest so far away from the crash when nobody else did? Any parallel to him ending up there in Season Five?
I think this may be one of the final questions answered, and perhaps one of the keys to unlocking the whole mystery.

How did Hugo get the nickname Hurley? Is it even important?
Hurley made a big deal of this early on, about how he was "not tellin'" anyone why he has that nickname. We've never come back to it. I suspect this could end up important based on something I speculated on in my last post about how so many characters have names, nicknames, or fake names that don't divulge their true identity. And I wonder if that could come to be important.
Related Question: What of the "Hurley Bird"? The producers have been awfully secretive about the large bird that flew out of the canopy twice calling Hurley's name (this was way back during the march where Michael led his friends into the Others' trap so he could get Walt back). It's long been my speculation that perhaps 1970s Hurley taught this bird to say his name during his days there, but who knows?

What do the psychic's prophecies and warnings about Claire's baby mean? Why can't Aaron be raised by anyone but Claire? (Or is it just important he not be raised by "An Other?")
Aaron has now had 3 mommies. And the MIB just told Kate that Aaron's mom is crazy, just like his own mother was. Could Aaron be the next MIB? Is this why there's always been this ominous feeling about that child? I think the real answer here lies in a DVD extra that I have not seen, but which a friend told me about. I never could wrap my head around how Mr. Malkin the psychic - right around the same period of time in 2004 - was so standoffish with Mr. Eko about no-such-thing-as-miracles and his own being a fraud, when he also seemed so convinced about Claire/Aaron, and tried so hard to get her on that plane. What my friend told me about is a deleted scene in which Malkin was paid a large amount of money by an unseen source to convince Claire to be on that flight. So perhaps the real question is: who most wanted Aaron to be born on the island? And was there really a concern about who raised him, or was that phrase just a way to scare Claire into not giving him up for adoption in Australia?