The first question to answer is what motherboard are you using?
If it doesn't support one or the other type of RAM, then your answer is obvious.
Between DDR2 and DDR3 the 'speed' difference is minimal. However, if you have more RAM it will be advantageous to your system if its heavy on applications.
At this point unless you already own a legacy system, there is not much point in getting DDR2. If you are building something new DDR3 should be the only choice.