Mysteries:

Why did Hurley and Miles have 'dead' people related Super Powers?
What was the kid Jacob doing, what was the point of that?
Why did the others call the smoke monster 'a sort of security system?'
Why did they create 'cerebus vents' for the smoke monster to move around? Who made the vents?
How could the smoke monster turn into Christian Shephard and Alex after he was already locked into the John Locke body?
Why did the numbers appear in so many non-island contexts? (The lottery, and everything in Hurley's life?)
The Valenzetti equation?
Why did Rousseau re-record the recording with the numbers? Why was the original recording in Hurley's voice?
Why did DHARMA use Egyptian hieroglyphs on the countdown timer at the Swan?
How did Yemi's plane make it all of the way to the island?
Why did the Blast Door Map say that the incident was in 1984/5, but the show then said the incident was in 1977?
Who was Magnus Hanso, and what was his connection to Alvar Hanso?
Why was the DHARMA film cut/spliced?