They are used to update your PS3's firmware if it is an older version that what the game requires. For example, GT5 requires FW version 3.55, so the PS3UPDAT.PUP file in the game is version 3.55.
If your PS3 is FW version 3.41 then when you try to launch GT5, the game will prompt you to update the FW. If you using a JB dongle or custom FW, you don't want to do this. Read some of the threads about modifying the EBOOT to prevent a game from updating your PS3 to a newer FW version.