There's a couple of first season mysteries that haven't been fully explained. Like the two old skeletons that were found, one man and one woman.
http://www.lostpedia.com/wiki/Adam_and_Eve
But this is definitely going to be answered because Damon and Carlton keep referring to it.
They're Kate and Jack. They could have returned to die of old age together on the Island. With all the temporal hijinks lately, what's to stop them?

From Lostpedia:
When all is said and done, people are going to point to the skeletons and say, "That is proof that from the very beginning, they always knew that they were going to do this."
I will say, though, that the first significant event in the show where we were thinking in the back of our minds that this is going to require a story telling element that isn't traditional narrative, is the discovery of Adam and Eve in the caves."