White-Gold's Stone was the Amulet of Kings. That was destroyed(?) in Oblivion.
Red's Stone was the Heart of Lorkhan (or possibly the enchantments on it / surrounding it). That was destroyed in Morrowind.
Snow Throat's Stone isn't ever mentioned I don't think - but seeing as White-Gold and Red have lost their Stones, is it far-fetched to think it was destroyed at some point during Skyrim? Walk-Brass is called "anthropomorphic", and it apparently literally does walk. If a Tower can be a person (which is my understanding of "anthropomorphic", it might not be correct at all) could a Stone be, say, a dragon? Or a soul, something like that?
And here's my last thought - does the Kalpa end when all of the Stones are destroyed? And if the heroes are destroying a Stone per game (at least since Morrowind) does that mean when we reach the last Tower... The series is done? Or at least the Kalpa is done?
~YAY TES CONSPIRACY THEORIES~