This is my "The Questions I Want Answers To Before the End of LOST".
These are more ideas than full blown theorems, if anyone wants more detail I'm happy to try and do a follow up post on why I think that.
(Assuming I have anything to base it on.)
I don't want to know that question xxx has been stated in "podcast 123" or "interview whenever" that the producers have said they won't answer it or they will answer it. I've tried to avoid things like that and hope no one will post anything like that on this page.
Section A: The Important Ones
This section is questions that I really want to know
A.1 What is the origin of the Jacob / MIB conflict?
- Jailer and Prisoner. MIB has been Jacob's prisoner, forced into protecting the island.
A.2 What have been Widmore's motives?
- Even tho this is A.2, it's the one I left to last to try and answer. I think it's because his motives are so beautifully ambiguous.
Idea 1: Widmore is on Team Jacob
- Everything he has done he has done for the good of the island, including sending the crew of the Kahana in season 4. Widmore genuinly believed that Ben needed to be removed from power for the good of the island. In a way, he was right as Ben killed Jacob at the end of season 5.
- Counter: Bram, who is definitley Team Jacob thought he was on the wrong team.
- Counter Counter: This could be evidence of infighting on Team Jacob, all working towards the same ends, but using different means.
Idea 2: Widmore is on Team MIB
- Since his exile, he has been in contact with MIB or his followers. Evidence for this is that Miles was warned by Bram and Ilana (who are definitley Team Jacob) that in working for Widmore he was working for the wrong team.
- Counter: He was exiled for having a child with an outsider and leaving the island regularly, not for being in MIBs thrall. If MIB end goal is to leave the island, it implies he hasn't left, then how could he recruit Charles?
- Counter Counter: Widmore could have allied himself with Team MIB without MIBs consent, aiming to get the Island Protector job that MIB offered Ben in Dr. Linus.
Idea 3: Widmore is Team Widmore
- Counter: This goes against the black and white duology that the show has been using, all the way back to the backgammon game in the pilot.
I'm leaning towards a combination of Idea 2 and 3, in thinking about 1 more, whilst it is possible it would spoil the Ben vs Widmore angle that has been building up nicely since Season 4. I think Ben and Widmore are two classic cases of power corrupts / absolute power corrupts absolutely. Furthermore, I think Ben is now the redeemed and Widmore is the irredeemable.
A.3 Why can't Ben and Widmore kill each other?
- They have both been baptised in the temple and are forbidden to break that rule. Much like Immortals in Highlander can't fight on holy ground.
A.4 What were the rules in The Shape of Things to Come? How did Widmore change them?
- In addition to being unable to kill each other, they cannot kill candidates. Alex Rousseau was a candidate.
A.5 What is the significance of the flash sideways timeline?
- The flash sideways timeline is what would have happened had the plane not crashed. More detail 
A.6 What is Richard's origin?
- Richard came on the Black Rock. Just say it already!
A.7 Who sent the periodic resupply drops?
- The Others pretended to the outside DHARMA Iniative that the purge never happened and they continued to supply the island. DHARMA was informed of an outbreak of something, that prevented them from sending new recruits. This is the reason for all the quaraneteen signs all over the hatches.
A.8 Who said "Help me" in the Cabin when Locke visited it first?
- This seems like a push from the MIB to send Locke along the route he went down. In addition the things flying around require a very similar power to what MIB used to free Ben in Dr. Linus. We already know that he can be very very small, e.g. Medusa Spider in Expose.
A.9 Who has been using the cabin and was it ever really Jacob's?
- I got nothing.
A.10 Who were Adam and Eve? How and when did they die?
- MIB and Jacob's original forms. Tho I admit it seems unlikely as Jacob was killed by a knife.
A.11 Why couldn't MIB kill Jacob? What was the loophole he found?
- The loophole was Jacob could only die if someone killed him of their own free will. It could be stronger than that tho, it may have needed to have been Ben as he was leader of the Others.
A.12 What are the whispers?
- Whispers are related to the Other's method of movement around the Island. See B.9. This is why Ben told Danielle Rousseau to run if she heard them.
A.13 Who was the boy in The Substitute?
- I got nothing, but wild ideas. A higher power or a young Jacob..
A.14 Why does Ilana state that the Man in Black is now locked in Locke's form?
- Because Jacob is dead.
- Because he stood in the water on the Hydra island.
A.15 What is Christian and what happened to his body?
- Christian is a representation of the Island itself. Tho I don't like this idea as it brings a third side into play.
A.16 What is the sickness / infection that has Sayid (and probably Claire)?
- As Dogen said, it's the internal scale being out of balance. See also C.4.
B Nice To Knows
Questions it would be nice to know the answer to but not as important as the ones in section A.
B.1 How did Jughead blow the survivors from 1977 to 2007?
- Maybe it was the will of Jacob? I don't realy have any idea and I don't think there is enough info given in the show yet.
B.2 What is Aaron's supposed significance?
- I got nothing.
B.3 How did the Black Rock get in the middle of the island?
- Not sure, maybe MIB threw it there when it landed. He did seem kinda annoyed that it was there in The Incident.
B.4 How did the statue break?
- The same reason the black rock ends up in the middle of the jungle?
B.5 Who shot at the boat during the time flashes?
- I got nothing. Hopefully we'll see this at some point in season 6 from the other perspective.
B.6 Why is Jacob bringing people to the island, and what is the 'end product' he is seeking?
- To prove that people can change. To find a candidate to replace himself.
B.7 Why did killing Dogen allow MIB to enter the temple?
- He was the guardian of the temple, with him dead the temple was just a place.
B.8 Why did Adam and Eve have black and white stones in their pockets?
- The stones represent MIB and Jacob, as seen in the cliffside cave scale.
B.9 How did Harper suddenly appear and disappear into the jungle in The Other Woman?
- The Others have a special way of moving around the island. This is referenced by Richard in Dr. Linus.
B.10 Who listed the Candidates in the Lighthouse?
- The Lighthouse is Jacob's list. Everything so far has associated Jacob with white and light.
B.11 Who listed the Candidates in the cliffside cave?
- This is MIBs copy of the list. Everything so far has associated him with black.
B.12 How was Sayid ressurected? Was that the intended result?
- It wasn't the intended result. If Jacob was still alive the baptism would have healed him, as it had young Ben back in the 1970s.
B.13 Whose eye did Hurley see in the cabin?
- Maybe Locke, Christian, MIB... not sure. Hedging my bets on this one.
C I'd Like To Know These...
Questions I'd like answers to, but think that they'll be left open.
C.1 How did Jacob / MIB get their powers?
- Prolonged exposure to the island? Aliens? Who knows...
C.2 Why was Walt so special?
- I don't think we will see Walt again. Perhaps his powers were similar to the ones exhibited by Jacob or MIB in their youth.
C.3 What is the origin and power of the Numbers?
- The numbers relate to important candidates. I think that is all we are getting.
C.4 Is the sickness/infection that has Sayid the same that affected Rousseau's science team?
- I think so, yes.
C.5 What's the reasoning behind the Other's burial rituals?
- Something to do with the MIBs use of dead bodies.
C.6 What was that giant bird?
- I have no idea
C.7 Why did Richard Malkin insist that Claire must raise her child by herself?
- He really was psychic and saw the consequences of Kate raising Aaron.
C.8 Why did some survivors go to 1977 after the Ajira flight and others like Sun and Ben stay in 2007?
- Only the candidates went back to 1977. This contradicts Ilana's claim that Frank is a candidate tho.
- People went where they needed to be.
C.9 Why were there pregnancy issues on the island?
- A side effect of the gas used in the Purge.
- The statue is of a fertility god, when it broke something happened.