Before proceeding, please make sure you backup your saves on a USB Thumbdrive. I came across this a few months ago when my PS3 was experience seemingly random bouts of lag on several of my games. I have a lot of games installed directly to my HD and it seemed at the time that only those games, and the games that installed data to my HD were the ones that were lagging. In order to fix my problem, a friend pointed me in the direction of restoring my file system using the PS3's Safe Mode feature.
For full instructions on starting your PS3 in Safe Mode, please refer to this guide:
http://us.playstation.com/support/answer/index.htm?a_id=1488
I don't know if this will work for you, but I see a noticeable difference in gameplay from before I restored my file system (just a couple of days ago) to now.
