Did you tried running your games with the lowest quality possible, just to know it it still does that?
Also, try looking in "power management" in the "control panel" to see if your hard drives shut down after some time of inactivity, I already had that kind of problem and taht solved it.
Are you running top quality with Half-Life 2? because I know that Half-Life works best with ATI than nVidia.
you can also try closing ALL system tray applications in Windows before running the game.
And when you have these slowdowns, does your HDD led lights up during the 3 seconds of hanging?