For XGL/AIGLX, there are still a lot of PCI and AGP cards (even many Intel onboard cards) that work great with AIGLX, which generally seems to have better performance and just be a better solution. The real reason you should get a PCI-E motherboard (unless you want two video cards with SLI, you only need one PCI Express 16x slot) is that PCI (for video cards) is long dead and AGP is dying--PCI-E cards are getting cheaper and cheaper, AGP cards are getting more and more expensive. Don't even consider getting an ATi graphics card, they have all sorts of problems with Linux, and are incompatible with AIGLX (but sometimes work maybe with XGL) due to --you guessed it-- crappy drivers.

You don't need a very fast card for the desktop effects, so you might wanna go with a budget card. I've had AIGLX running on Intel onboard and on an old NVidia FX5200. All you really need is a modern card with 128+MB of video RAM. There are some chipsets that come with an NVidia 6100 as onboard; those would probably be fine (they're PCI-E, so upgradeability is good if you feel you need something beefier).