What to do when your computer lags and there are no viruses/malware found.

Sometimes Windows may start strangely lagging. Open programs become non-responsive for a few seconds or tens of seconds, and you may see the hard drive light flashing rapidly or being lit continuously. This may be caused by a few factors.

Let's assume that there is no malware infection in the system, and there's adequate antiviral protection running. Let's also assume that the hard drive of the system is in good health.

If the PC start up is extremely slow, with hard drive light constantly lit, and all programs loading very slowly - it may be due to a "DMA step-down" - Windows is designed to step down one DMA speed after it encounters a hard drive transfer error, which makes everything work very slowly because of the drive transfer limitation.
In Windows XP - this can be resolved by running a small DMA reset script (available here - download and run the VBS)
In Windows Vista/7 the resetting of DMA speed can be achieved by going into Device Manager and deleting the IDE ATA/ATAPI Controller and letting Windows re-install it on its own.

But what if the DMA speed is correct and Windows is still lagging badly? Then it's time to dig deeper and see what keeps that hard drive so busy. A good tool for that is Sysinternals Process Monitor (available here). It shows the "behind the scenes" of Windows running processes and may let you see what is hanging up the system so badly. After running Process Monitor, go to Edit and check "Auto Scroll" to let you see the process logging in real time.

What you should look for is the "WriteFile" operation - it may come in big bunches. Identify the process responsible for it and check out what application is executing all this data writing. Removing or re-installing this application may solve the lagging problem.