It's a difficult question, after you get past the big two (4e & 3e), and even for those two, we don't have any hard data about which is the most played (or if that distinction can be made).
My personal, anecdotal experience has been that 4e is the most played, 3e is right behind it (though descending)...and then there's a big drop. From there, you've got World of Darkness, Mutants and Masterminds, GURPS and Hero in no particular order. While I agree that conventions are hardly a good measure, they do act as at least some relative indicator of popularity, IMHO, if not an indicator of their popularity relative to each other.
By the same token, Gencon is going to be disproportionately in favor of D&D, while some conventions are going to be disproportionately against it. For example, if I were to go by my experience of Gencon, Origins and Dreamation this year, then I might think that Dread is one of the most popular RPGs on the market. And while I think it is a indie game darling (and rightfully so, I might add), I think its penetration in the market is incredibly small.
The issue of purchasing gaming materials without the intention of playing them (or the inability to do so, due to circumstance) is another question entirely. I have a bookshelf of GURPS books that have never seen active play, but were great research materials and reads. The same is true of a lot of games I have. WoD and GURPS, in fact, are famous for having materials that are often purchased without the intenion of play.