The DDR3 will definitely be faster but it all depends on what your doing with it..
If it's mainly for gaming then the DDR3 will definitely be the best choice..
But if it's just a Internet Browser/email machine then the DDR2 would do just fine..
I'd stick with the DDR3 though, I have 8GB's of DDR3 in my newest rig and I definitely don't regret buying it..