I have had a similar problem, and it was caused by a hard drive about to fail. The drive is trying to read the same bit over and over again, which hangs the system temporarily as it's an operation that would normally take milliseconds. Eventually it succeeds and everything looks normal. (The hard drive light being constantly lit or blinking, or grinding/ticking noises from the drive, while the system seems hung is a 100% indicator of this.)
Reinstalling Windows would shift the files around on the drive somewhat, which would cause the "bad" area to be accessed more or less frequently. You can see why this would make the problem happen less often (or potentially more often).
Try running a comprehensive drive diagnostic (surface scan) or just try a different hard drive if you have one. You should also check your backups. Once a drive has developed a fault it is generally only a matter of time before it breaks down completely.
Bad RAM could produce similar issues but in my experience bad RAM usually tends to cause hard crashes rather than stuttering/freezing. Then again swapping RAM (or taking one stick out as was suggested) is a lot easier than swapping drives, so try that first and see if it helps.
SD, try Google Chrome. I wouldn't touch IE6 with a long pole but Chrome is really quite speedy and not quite so outdated security-wise.