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.
Actually the primary difference is in how the data is read out of the chip. DDR addresses two rows of data at a time and outputs the data over a period of two clock pulses allowing it to output the data at twice the rate of normal DRAM chips. DDR2 addresses four rows at a time and outputs them over a period of four clocks. DDR3 addresses eight rows and outputs them over a period of eight clocks. DDR4 will double the number of rows addressed again to 16. Anyone wanna take a guess as to how many rows are addressed by GDDR5 memory chips.