well as far as desktop fans running all the time, you can mod the case and the fans and what not so you have control over them, but it is a good idea to keep the fans on (plus the fact that the power sup. fan is always running). Notebooks have 1 fan that is on all the time (most do anyways).
Processor speed: There will be ALMOST NO resonable difference in your performance based on processor speed. What will determine the speed of your system will be (Depending what you will use the system for) RAM, HDD speed, Vid. card speed, etc.
Hope that helped.