Jack first discovered the caves in "White Rabbit", but Adam and Eve weren't seen until "House of the Rising Sun", when he and Kate stumbled upon them after escaping from a swarm of bees.
Locke gave the skeletons their nicknames, taken from Adam and Eve of the Bible. However, given the mother-son relationship between them, a more apt analogy would be Eve and Cain.
Jack neglected to mention the stones when Locke asked what had been discovered. (see also: Black and white)
Jack guessed that the bodies must have been dead 40-50 years based on the deterioration of their clothing. ("House of the Rising Sun") However, upon discovering the remains of a Nigerian smuggler, Locke told Boone that normal clothing would decompose within 2 years and that the high quality polyester on the smuggler's body would take 2-10 years to get to its current condition. ("Deus Ex Machina")
In 2007, when Hurley and Jack revisited the caves, Hurley theorized that the skeletons might belong to two of the survivors of Oceanic Flight 815 as a result of time travel. ("Lighthouse")
In a March 2008 Underground Online article, the producers talked about how the skeletons might give insight into the nature of the show and evidence that certain elements were planned early on.
In a March 2009 Sky1 interview, the producers confirmed that Adam and Eve are not the actual biblical figures, and are "not the dog either."
In January 2010, after Barack Obama and his administration moved their State of the Union Address away from February 2 to avoid a conflict with the premiere of Lost's final season, Damon and Carlton said that Obama could ask a question about any unresolved mystery and they would answer it. Over Twitter the White House's ABC correspondent, Jake Tapper, claimed that Obama had asked the identity of Adam and Eve. In reply (also over Twitter) Carlton said, "Good question! Have POTUS call us!" [1]