i'd say go for 6GB of DDR3 . I wouldn't think there would be much difference between the two but DDR3 will obviously be Faster. If its for games the more memory the better.
If its price you're worried about go for the 4GB of DDR3 and You should be able to add more after a while, DDR3 is an upgrade we'll all have to make at some stage - i'd see it as a waste of money to buy a ddr2 mobo then having to upgrade again to ddr3. Though i have heard of mobos that support both types of memory
hope this helps
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..