Players can get Justice Points (normal dungeons) and Valor Points (heroic dungeons) by doing the Cataclysm dungeons.
However in the past players could buy pvp gear with the extra badges, now we don’t have what to do with them as Blizzard decided to not sell even jewelcrafting stuff or chaos orbs.
Considering the past, when they will release the new tier set, after this one, players will be able to buy the current epic gear with Justice Points (the normal dungeons version), and the next gear with Valor Points (heroic).
It won’t be in 4.0.6 for sure since the game already started and only few guilds managed to clear all the content.
It will be in 4.1.0, the next major patch that will add season 10 for pvp and a new major raid for pve-ers.
Until then.. What to do with the extra Valor & Justice Points? Just keep your Justice and Valor points being caped just to make sure you have them if Blizzard will add free gear or at least do the same thing they did in Wrath of the Lich King, adding gear for sale for badges from the last patch content.