Intel is the only company that supports free graphics. It's got a fully free
driver. Works great with 3D.
AMD (ATI) has released parts of the driver under a free license. The fully
free driver is not good. No 3D and artifacts.
Nvidia hasn't co-operated at all. However, there is a reverse engineered free
driver that can do 3D.
So, if we only look at graphics cards, Intel is the way to go. But on the
other hand Intel wifi cards are notorious for not working with free software.
And replacing the wifi card with a supported card is tricky since many
vendors have short whitelists of wireless cards they only accept and the user
has to possibly crack his own machine (BIOS or the wifi card) to be able to
use a non-whitelisted wifi card.
http://libreplanet.org/wiki/Group:Hardware/Mini_PCIe_slot_restrictions_on_wireless_cards
It is really hard to know what to go with...