I used to install all of my apps on there own partition. However, if you have to reformat, or re-install the main OS all the file associations to the apps are lost, so it really didn't make a difference as the apps had to be re-installed anyway. I now keep all apps on the C: drive, and all of my actual work on a external firewire drive. This seems pretty stable, and allows me to run a reletively small main HD, so running things like scandisk, and defrag are quick.