PCI-E doesnt make something better yet......there is neglible difference in performance between a 6800GT AGP and a PCI-E one....
the two cards your comparing are totally different tho, one is barely a DX8 card, the other is a DX9 but with very low clocks and pipes.....
my 4200Ti was a nice little performer with only 64mb...on older games i'd imagine it'd have better framerates than the newer X300SE.....but on newer games it might fold up a little.......
thing is, you either have a AGP based system or a PCI-E system..... so comparing those cards is pointless...if your AGP based you need the 4200, if ur PCI-E based you need the X300SE..
my advice, whichever you have, AGP or PCI-E, save up and get a 6600GT 🙂
(btw, your not confusing PCI-E with PCI are you? honest question, i see your a golden member here so i'd assume you know, but just asking in case...)