Let me just dispel one myth.
When you load an application, almost always, it creates entries into the operating system registry, which is normally on the C: drive.
If you subsequently have to carry out a clean install due to corruption of the operating system, all these entries will be lost, so even though you may have chosen to load these programs on D; or E; or whatever, they will not work and you will have to reload them again. Therefore, there is not much point in loading applications anywhere other than C:.
The ideal way to protect your system, is to invest in something like Norton Ghost or Acronis Drive Image, and save a complete image of the drive, to your other drive. That way, if push comes to shove and you need to reinstall, you can normally copy an image back to C: in about 20 minutes, depending on how large the image is. But keep in mind, you will only recover what was on the machine at the time the image was made.
Make sure all your personal files are on the drive not used for the operating system. Again, if you have to reinstall from a clean base, all your personal files will remain intact if they are on a different drive.