The argument for PCI-E is getting stronger, in any machine you consider may be worth fitting a graphics card upgrade to in, say, a year or two's time. By then, it's possible that the PCI-E slice of the cake will be bigger.
At the moment, it really makes little difference - if PCI-E 16x is theoretically faster than AGP 8x, we aren't stressing AGP 8x fully yet. If you see Nvidia SLI as the future, instead of a stopgap before more powerful cards, then maybe PCI-E SLI capability is a feature you should have.
For the non-gamer and light gamer though, the Radeon Express 200 chipset looks a potent solution, with onboard graphics that are finally worthwhile.