My personal preference (for fun) is to have an "extremely clean" computer installation after I have experimented with a number of software programs, fun video effects, and configurations. After I have figured out exactly what I want, then even if it is not necessary, I may just reinstall Ubuntu (or Edubuntu) Linux, because it is so easy to reinstall and reconfigure. The whole thing may take less than a couple of hours (more for Edubuntu), depending upon circumstances. If you do this either for fun or else for some reason you need to do it, I recommend that you use a manual install (from the install CD or USB drive/flash disk) to install Ubuntu over the same disk partitions that you used before. Be sure to choose "format" the Ubuntu partition when you do the install so that you will truly have a "clean" install. Also, I typically do this whenever a new version of Ubuntu comes out (twice per year), although it is absolutely NOT necessary to do this. When a new version comes out, Ubuntu will offer a button on the Update Manager window to simply click on.
To Achieve the Greatest Stability and Problem Free Operation
When you either install (or upgrade) Ubuntu, use the latest version that has been out for at least 4 months. Upgrades to Ubuntu occur very fast, and Ubuntu is known for being very stable and trouble-free. However, like any software product, rare or overlooked problems may be reported and fixed shortly after any given version has been released.