Unless your motherboard supports both ddr2 and ddr3 it's a mute point you can't put ddr3 in ddr2. If your thinking about upgrading motherboards and processor then go with ddr3, but not worth the money for small amount of performance increase just for faster memory.
The primary variable of importance for memory is the speed, DDR3 1600 MHz will generally be faster than DDR3 1333 MHz regardless of timings (but not always as we will see later). Of secondary importance is the timings -- CAS 7 is faster than CAS9. Take a look at this chart for DDR3 memory showing the relative performance of DDR3 RAM with different speeds and timings: http://www.tomshardware.com/reviews/core-i7-870-1156,24...
The key to remember is that memory is seldom the bottleneck in any system. The only reason to get memory with higher speeds is so that you can overclock your processor, and get a little performance boost from your memory.
So, to answer your original question, DDR3 running at 1600 MHz with CAS8 will be faster than DDR2 running at 800 MHz with CAS4. But you really are comparing apples and oranges, and you cannot make any general statements that will be true in all situations.
Thanks for your answer dpaul8. As the situation goes i have that ddr2 reaper ram and am buying a new board and pii 955 to go with it. I was tossing up between getting a ddr3 board and then needing to buy new ram or grab a ddr2 model and keep my ram and save like $150.