Who took the Zodiac boat from the beach? And who shoots at our time skippers from an outrigger? Why do they shoot? Did Juliet hit / kill one of them when shooting back?
Theory:
It would stand to reason this was Ilana's group (we know they were 316ers), but who knows?

Why did Sun crash with Ajira 316 in 2007, and not get flashed out into 1977 like Jack, Kate, Hurley, and Sayid?
Theory:
Uhhh, maybe because it's more rewarding in the end to keep Sun and Jin separated as long as possible? Sure hope it's not something as contrived as that, though...

UNANSWERED (And I Personally Doubt We're Gonna Get An Answer)

Why was the faked Oceanic 815 crash site in the Indian Ocean - northwest of Australia - when Sydney-to-LA flights take off from Southeast Australia and flight in a northeasterly direction?
Why did anyone back in the real world believe the crash site was on the level? There should have been no way this flight would ever have been in those coordinates.

Where does Ethan's seemingly-superhuman strength come from?
Remember the time he picked up Charlie with one arm and pinned him to a tree? And how he carried off a fighting Charlie and Claire by himself? And how easily he bested Jack in their first fight? What was that about? And how was Jack able to best him the next time they faced?

Where does Walt's luck come from? Is there truly something special about him? Can he will events to happen?
"My dad said I'm the luckiest person he ever knew." This quote from Walt is strangely echoed by the Hurley character in the Season Six premiere. Sadly, I think LOST wrapped up the Walt storyline in Season Five, when Locke and Abaddon visited Walt in NYC and Locke decided Walt "had seen enough." I love this show, and have great faith in the producers, but the apparent dead end of the once-so-promising, once-so-prevalent Walt story might just be its greatest failure. I believe they just got to a point in the storytelling where they realized they had to move on with other things, and that they just couldn't go down this road, too.

Is there more to the story and meaning of Kate's toy airplane?
Okay, I admit, this one is more of a personal bug up my rear than a mystery. I just still can't fathom the lengths Kate - already a fugitive from the law - went to assemble a team of hooligans and rob a bank, shooting people in the progress, to retrieve a TOY AIRPLANE from a safe deposit box in New Mexico. I don't care how much guilt she had over her buddy's death, these are just not the acts of a sane or smart person. So I insist there has to be more. But sadly, there isn't.

Why do some compasses work just fine on the island, and others (like the one Locke once gave Sayid) don't?
We know about the huge pockets of strange material under the island that cause a magnetic anomaly, but then why don't ALL compasses fail to work?

Was Sawyer's boar really the spirit of Frank Duckett come to let him off the hook? And how did the whispers know to say "It'll come back around" to Sawyer? Where would they have gotten such personal knowledge? Did Smokey ever memory-flash Sawyer?
The first part of this question is tricky because in one sense it doesn't matter. Sawyer probably believes as much, having been conditioned to do so by Locke's story about his foster mom, foster sister, and the dog, and because he would like to believe it. But did the island really make it happen? Was the boar Smokey? If not, how did the whispers know what they know?
Similar question to above: Did Jack really hear Christian through the "broken" Hydra intercom telling him to "let it go"? If so, how? The whispers again?

Walt asked his dad if once the raft is rescued, they will send help back for everyone else. Michael says yes... but he already has ascertained that "finding this island again... might be difficult." How does he know? Just because they haven't been rescued yet? That could be explained by how the pilot told them rescuers would be looking in the wrong place for them.
Isn't the more logical assumption at this point that the island IS able to be found, since they've encountered other people (like Ethan) on it?