First, which operating system are you using. There are some processes that can be terminated in vista that don't even exist in XP.

Second is this a brand name computer (dell, xp) or is this a computer that you put together yourself. If it is brand name computer it is likely to have a whole lot more crappy apps running in the background then a fresh install of windows.

Third, how many wow accounts are your running? what kind of CPU do you have (speed, cores)? how much RAM do you have and what kind? what is your graphics card?
This may seem irrelevant, but if something is not up to par, when windows needs to run periodic tasks, that is when you are going to notice the low FPS.