I have never heard of any problem pertaining to the support of PCI Express.
The best you can get today are the motherboards that LibreBoot (a free BIOS firmware): http://libreboot.org/docs/hcl/index.html#supported_list
Unfortunately, there is no solution for current/future x86 architectures: http://libreboot.org/faq/#intel
ARM may rescue us though.
