With Sony releasing Trophy support for their console, some games in your backlog may be getting patches to add the support in.
Pain has new set of trophies, completely unrelated to the ones you may have been earning in game already (also called trophies). The in-game trophies unlocked new skins for the primary character, while the Playstation Trohpies are added to your Trophy Score. The Playstation Trophies are only mentioned in your PSN Trophy case and there is no mention of them in the game.
Uncharted also had a built-in unlock system. They unlocked various extra information, artwork and other unlockables. They are built into the game and interface. However, you must earn them again if you have unlocked them already.
So, which system do you prefer? Games that patch to offer new trophies and assume the old were already achieved, but add clutter to the interface? Or games that patch into their more elegant pre-built-in system, but requiring a replay through the game?