That's why it's usually a good idea to have a second hard drive or partition your main hard drive.
A (relatively) small partition, 20GB is sufficient, which is used for Windows (or whatever OS you use) and the programs that you've installed, plus a second partition for all of your other files - pictures, movies, songs, text files, etc.. This way, if you do have to do a clean re-install (which the "experts" suggest you do at least once a year) none of your important files are affected.
I tend to keep the installers of any programs I get on a separate drive (my system has three) so that I will still have them to re-install, should the need arise. I hate having to try to find those great little programs that I absolutely need but can't seem to remember the names of (like that one that does this thing...oh, or the one that does that - can't live without that... now, what was that called, again?)
Of course, backing up to disc is very helpful, as well.