Jonathan,
Good questions.
Xilinx PCI designs come with design files and support files necessary for simulation and implementation. This is so that users can hook up the PCI core to their FIFOs or other back end logic. So the PCI design can be integrated with the rest of your design using a standard black box flow supported by synthesizers, etc.
There are quite a number of companies building various flavors of general Virtex boards for resale, many using a PCI interface. I'm still trying to verify which companies have announced such boards.
Meanwhile let me point you to a few companies who make various general boards with Xilinx parts on them:
Annapolis
Micro Systems
Avnet
Design Services (announced)
MiroTech
Microsystems
Nallatech
Limited : Embedded Electronic Systems
Virtual Computer Corp
XESS Corporation
I hope this helps,
Dennis Rose