DDR3 will eventually outpace DDR2, yes, but you're looking at spending a lot more on DDR3 and added price does not justify the extra performance -- most benchmarks you'll find out there show maybe a 2-3% difference at best -- unless you're using this for memory intensive software or trying to save energy (DDR3 uses less power than DDR2).
If this machine is just for gaming, video editing, image editing, etc. more gigabytes of DDR2 RAM will yield you better results than less gigabytes of DDR3.