What is you budget? What do you do with the computer? How long do you expect this purchase to last?
Only the top end graphics cards make use of most of the bandwidth of PCIe1 slots. A mid range card generally uses less than half - which leaves plenty of room to upgrade to a better card later without worrying about PCIe 2.0.
To fully suport 2.0 cards later, you would need to purchase a board with the X-38 chip. As these were just released this month, there are few boards that have them and they are very expensive - I think about $300+ compared to about $120-$150 for a good PCIe 1 mobo. So generally I would not look for one now unless you have a large budget and/or want to be able to upgrade later to a high end graphics card that will then cost you $300 or more - or in other words you are a high-end game player.
PCIe 1 and 2 cards and mobos are compatible. However if you use a PCe 1 card on and PCIe 2 mobo, the card will not be able to use the full bandwidth of the mobo - it will still run like a PCIe 1 card. Conversely, a PCIe 2 card on a PCIe mobo will be constrained to the bandwidth of the mobo - but you may still enjoy the other advantages of the card - which may include faster internal memory and improved instrucition sets and other features - such as HDCP if it has it.