What mainboard is it ? I assume you mean PCI-e as a year old PC with only PCI-X slots would be weird and you'd be extremely limited in choices of GFX card you could plug in ;)
For PCI-e really for the mainstream you are limited to either Nvidia and their closed source binary blob or ATI/AMD who despite now trying to be OSS friendly have never managed to provide me with a satisfactory experience (on Windows or Linux but especially on Linux)
Myself if I have wanted 3D and accelerated video etc to just work I have used nvidia and their binary blob, if I just want a reliable desktop machine with enough oomph to maybe handle a composting window manager then I try and find something with a compatible intel gfx core but you can't get those on a GFX card.
There are also two alternative OSS drivers for nvidia "nv" which was developed with/by nvidia and is now discontinued and doesn't support the modern chipsets or nouveau which is a product of reverse engineering and only really supports 2D acceleration at the moment (so any compositing desktop ideas are out) it may work well enough as a general machine not sure what video performance is like though.