For machines that slow down over time, we generally recommend reinstalling Windows from scratch about once a year — unfortunately, that means that you’ll have to reinstall any programs that you’ve installed.

If you’ve installed a lot of programs onto your machine, especially programs that customize the way Windows looks and functions, they may be weighing down Windows and slow it down right off the bat. Uninstalling some of them will help, or you can use Autoruns from Microsoft to turn off a number of the programs that run on your machine at startup. You can download it here: http://www.microsoft.com/technet/sysinternals/utilities/Autoruns.mspx

There’s actually more than one form of bitrot. If you’re talking about the gradual corruption of the software due to operating system errors, bad information or other such software-related things, the only way I can think of to prevent bit rot is to not use the computer, unfortunately. The Windows operating system reads and writes information to and from the registry many times each day, and other programs also put information into the registry and change it. You can try to avoid installing new software that you don’t really need, and if you practice safe computing you can avoid getting infected by nasties that will corrupt other parts of your computer you’ll definitely be on the right track. But avoiding the problem completely? It probably can’t be done. You could try using a registry cleaner program semi-regularly, but I’m not sure it will be of any major long-term help.

The other form of bit rot is caused by degradation of the physical media. That can be caused by the material in a floppy, CD or hard drive breaking down over time, or by a gradual change in the magnetic state of information bits on the media. This is basic physics and chemistry at work here…so there’s not really anything you can do to stop this.

Your best hope may be to back up your system regularly. Unfortunately, that’ll back up any errors that may have accumulated along the way, but if things go spectacularly badly at some point, at least you should have one good backup point to go back to.