As of the latestupdate to this Answer Record, the Xilinx cores for PCI Expressonly supportone virtual channel. However,you should check the data sheets for the targeted core for the most up-to-date information. The Virtex-6 and 7 Series cores and future cores will support the Virtual Channel Extended Capability set, which allows the link partner to support traffic class prioritization, if desired. However, the core still only supports one virtual channel.
08/12/2011 - Updated to mention cores only supportone VC