Pretty much what they said, 4 or 5mm is the norm for side/rear windows. 1 or 2 is too thin really, unless it's being heavily curved.
The best method of cutting it I've found's a router, although that's with polycarbonate. (I'd definitely recommend using polycarbonate (lexan) not actual perspex as it's much less brittle.)
Personally, if you're ever going to leave the car in a public place I'd want 4mm minimum and bonded to the shell, not just fitted in the rubber seals.