Because Sony's trophy system is only being implemented now, a bunch of games have already been released that don't make use of the feature. Meaning developers will need to go back and bolt on trophy support in their own time. So when 2.40 becomes available, which games will have them, and which ones won't? While Sony released a preliminary list of titles that will be the first to implement trophies the other day, they've since added one more: our 2007 NQGOTY, Uncharted: Drake's Fortune, which "will also receive a patch at some point in the foreseeable future".
Sony's Eric Lempel Talks PS3 Version 2.4 [GameSpy]