Not that I know much about this, but my first suspicion is the virus scanner, particularly if it's Norton or McAfee. Might try it with any active scanning turned off or even shut down entirely to test. (An earlier version of McAfee I had would freeze the mouse pointer for a quarter sec every 2 seconds, talk about maddening.)
The increasing badness of the problem also suggests some kind of memory garbage collection. The fact that you turned off extra programs tends to discount this, though. Might try running a CPU meter of some kind to see if any programs keep spiking, or if it's the game itself. That it hits all your games makes me think it's a general memory management problem, though.
Probably not much in the above you haven't thought of already, but hope it helps.