Modern motherboards/chipsets are going to use DDR3. DDR3 is a bit faster while using less power. The power differences are barely measurable along with the real-world performance differences.
One of the main differences is price. DDR3 (while being better) is much less expensive than DDR2 due to supply and demand. Everyone is producing DDR3, and with modern support for only-DDR3, it is the ram to go with.
If you're worried about performance of DDR2, don't be.