PCIe slots are backward and forward compatible. That is if you install a 3.0 card on a 2.1 (or lower) motherboard, the card will work at the highest availble speed/bandwith limitation. Likewise, if you installed a 2.1 (or lower card - not that you'd want to), it would operate at its full capacity in the 3.0 slot.
If you want to take it from the horses mouth on this, here you go:
Q: Will PCIe 3.0 products be compatible with existing PCIe 1.x and PCIe 2.x products?
A: PCI-SIG is proud of its long heritage of developing compatible architectures and its members have consistently produced compatible and interoperable products. In keeping with this tradition, the PCIe 3.0 architecture is fully compatible with prior generations of this technology, from software to clocking architecture to mechanical interfaces. That is to say PCIe 1.x and 2.x cards will seamlessly plug into PCIe 3.0-capable slots and operate at their highest performance levels. Similarly, all PCIe 3.0 cards will plug into PCIe 1.x- and PCIe 2.x-capable slots and operate at the highest performance levels supported by those configurations.
2.1 and 3.0 are almost identical. The only difference is the bandwidth. While it is true that there was a problem with some Radeon cards, this was specific to the electrical interface in the 1.1 motherboards; they lacked the support for power efficiency. Most mobo manufacturers have updated their BIOS to add support for 2.1 cards on their 1.1 boards.