I think some gameshark,Action replay,ect uses some USB stuff. You can load exploits from USB thumb drive using newer versions of swapmagic. Headsets from Socom might use it? Don't know about that one. Maybe some racing wheels? IMO it's a feature Sony added which was never really needed but they put it in just in case. Half of the ports on the newer gen consoles coming out probably won't be used either.
BTW I heard there is a new app out that allows you to hook a external HDD to boot games from(made mainly for the Slim version) HDD.