If the slowdown isn't obvious in Activity Monitor, then it will take some sleuthing on your part to sort out your particular set of circumstances that is causing it: Spotlight indexing, downloading, anti-virus, printing, etc.
CPU usage percentage isn't a complete indicator of what could be bogging down a machine. I once had McAfee Anti-Virus completely bog my machine down (and I mean the beachball, freezing screens,a nd almost complete inability to finish the boot process for an hour at a time) trying to scan the contents of my iDisk contents. But the five processes being run by AV never got above 2% or 3%. Once I disconnected my iDisk, all was fine and I don't hear a peep out of AV.
It is no secret that Mac OS X is a memory hog, and the occasional reboot (I do so every Monday morning) does wonders.