Hi, I am getting ready to rebuild a new machine too and have looked very hard at this issue. I want to buy the new Intel X38 chipset that you can buy in either flavor. One board, the Foxconn X38A, actually supports both DDR2 and DDR3. So you could buy the DDR2 now and wait till the prices come down in a few months and slap in some DDR3. That's what I was going to do, but after visiting a few Over clocking and more game oriented hardware review sites/forums. I have decided against that and pick up a more performance oriented MB that supports DDR2 only. Those forums are big time computer enthusiasts and they feel that DDR3 just doesn't give you enough of a performance gain to justify the higher prices.
The MB is am considering is the Gigabyte GA-X38-DQ6. Has the new pcie2.0 which increases the bandwidth for the graphics card (but you have to get a graphics card that has it too).