I know Jon has one of these in his rig, but what songs does he use it on? I've been trying to pick it out for ages but can't figure it out...

It might be hard to figure out but I think he might have used it on older stuff like Spies and Shiver, Daylight also comes to mind too but thats just a total guess...

 

Its a very rare pedal something like only 500 were ever made.

That's what I would have thought too. However, Jon didn't start using that pedal until 2005 by which time most of those songs were phased out of the band's live set.