When this happens, does your hard drive led(light) on the tower blink allot. Sometimes you may be loading the next section of a game(textures and whatnot) while playing. It could also be the page file being written to / read from.
To make sure its not the game. when it happens and stops, can you still go to the same sport in the game without it happening again? It so, it may be loading or paging.
I would recommend closing ALL un-needed programs when gaming as this can cause windows to need to write data from memory to the hard drive when the game requests more memory space.
It should be noted that some virus scanners(well most) scan in real time and if your game loads textures/meshes/sounds while playing, then they have to be scanned first, this adds to the lag for some systems. You may wish to try to add the game folder to your virus scanners exude or ignore folder to test this out.
If you have windows Vista or 7(the 64 bit ones), it may be worth adding some ram to that system, with XP it may not be worth it as XP and any 32 bit operating system (this includes windows Vista 32-bit and Windows 7 32-bit) will not address more then 4GB of total memory and that includes parts of the board and video memory so more like 3.0-3.5(tops for the most part) of memory.
You can use the task manager(ctrl+shift+esc on the left side of the keyboard) to see how much memory your system is using as well, but if you tell us what version of windows you have, we can provide more detail on how to read the task manager information.