This is an idea that alot of people have been kicking around for a while, and I thought that since no one else was doing this, that I should go ahead and get it started. Obviously, no matter how long my list is, it won't BEGIN to graze the surface of all the loose ends LOST has left open so far. But alas, here is the list. Please pose questions (or answer some) of your own that I haven't displayed, and I will (with the power of Edit) add them to this list. Thanks.
(1) Who is Jacob?
(2) Can Ben control the Smoke Monster? How?
(3) Why is Widmore so confident that Ben won't find Penelope in the Flash Forward?
(4) Why does Widmore want the Island?
(5)
What is the device on Keamy's arm?(6)
Who is in the coffin that Jack visits during Through the Looking Glass?(7)
How did Ben end up in the Sahara Desert in the Flash Forward?(

In the FFs, Who does Ben have Sayid bumping off?
(9)
Why is Claire not one of the Oceanic Six?(10) Is Jin really dead, or is his tombstone farce?
(11)
Why does Sawyer remain on the Island?(12)
What will the Survivors find in the Orchid Station?(13) Why did the sky turn purple in the Swan Station explosion, and during the Wheel spin?
(14)
How did Desmond and Locke survive the Swan explosion?(15) In the FF, what is the favor Kate does for Sawyer?
(16)
How did Sun survive child birth if her baby was conceived on the Island?(17) What is the significance of the 305 bearing between the Freighter and the Island?
(18) In the FB, why was Richard Alpert so upset when Locke chose the knife and not the Book of Laws?
(19) Why does Richard Alpert never age?
(20)
Why is the Island keeping Michael alive?(21) Who else has this Immortality curse besides Michael? {At least, temporarily}
(22) What significance does the Bible verse Eko reads to Locke have? In it, he mentions the Book of Laws, and the Temple... what does this all mean?
(23) Is Mikhail dead or not?
(24) How is Christian so close to Jacob?
(25) Who planted the farce 815 at the bottom of the ocean?
(26) When Widmore says that all of Ben's possessions were once his, what exactly is he referring to?
(27) Will the Island be moved physically, or through time?
(28) Who does Abbadon work for?
(29) Why must only Claire raise Aaron? Why does Claire tell Kate not to dare bring him back?
(30) What is the story behind the four-toed foot of a now-missing statue?
(31) What exactly is the Smoke Monster?
(32) How was Desmond granted the power of foresight?
(33) Why do certain people receive psychic images of Walt?
(34) In the future, why does John Locke go by the alias Jeremy Benthum?
(35) In the FFs, where did Sayid move Hurley?
(36) In the FFs, what is it that Sun is offering to assist Widmore with exactly?
(37) Did Jin survive the freighter explosion?
(38) What is the significance of Christian's ghost? Has he become an Angel-Of-Death knockoff?
(39) Why was Ben transported into the future after spinning the Frozen Donkey Wheel?
(40) Where did the Island go once the Wheel was spun?
(41) What did Miles mean when he referred to Charlotte's "getting back here?" Where is "the place where she was born?"
(42) What is going to become of Daniel Faraday and those adrift with him?
(43) How does Locke go about getting off the Island and posing as Bentham?
Argh. I can't think anymore. Please, give me more questions to add, or any answers to questions that I have displayed. Note: Please attempt to stay away from theories.
Okay, below are the questions that have been asked AND answered:
(5) A heart rate monitor; when Keamy's heart stops beating, it triggers the C4 that is on the Freighter.
(6) Jeremy Bentham... or, as we know him, John Locke.
(7) The effects of the Frozen Donkey Wheel transported him into the future; why that particular place, that particular time, I do not know.
(9) She didn't make it onto the chopper, and they never got a chance to go back to the Island.
(11) He jumped off the helicopter to let off some weight, and swam back to the beach (losing his shirt along the way).
(12) Not only does it hold a time travelling machinism, but it also is the home of the Frozen Donkey Wheel.
(14) The Island chose otherwise. (kinda corny, but we'll go with that)
(16) She escaped the island before her third trimester, therefore missing the "deadline," no pun intended.
(20) He had not fulfilled his purpose: to stall the bomb long enough to get the helicopter off the Freighter.