I will be building a new system- eventually, but there is no point in spending a lot of money now when PCI-E R2 compliant motherboards and graphic cards are "just around the corner". I understand PCI-E R2 doubles the bandwith of PCI-E R1. I can wait a quarter.
While it is (likely) true that PCIE 2 doubles the bandwidth, most cards don't take full advantage of the bandwidth now, so it is not really worth waiting for unless you plan to get the best card available.
To answer your original question, I believe the next Nvidia cards (coming Nov 12) will be PCIe 2 compliant.