This is going back aways. The theory was that Thomas -- Claire's artist boyfriend and Aaron's bio-dad -- was actually Ben, in a time-warped twist before Ben came to the island. That is why "the Others" wanted baby Aaron -- cus it was Ben's (aka "Thomas") kid.
Aside from an eerie resemblance and the appearance of Thomas-esque art in the Swan hatch (both created by Lost director Jack Bender), this stupid theory didn't have much to it (as stupid theories are wont to not -- huh?). It got especially weird when people started thinking that Aaron was Ben, too.