It will make a difference if you have an uber overclock.
If for example you push a Q6600 Past 3.6 Ghz, the DDR2 1200 will be slightly more stable, only because it was designed to run at 1.2 Ghz while DDR2 800 is only designed for 800 Mhz. In the end most processors are not pushed that far past the allowed front side bus for whatever motherboard your using. This is of course unless your using Phase change or something more extreme.
DDR2 800 is more than enough even for my 3.7 Ghz overclock..