I remember when I jailbroke an iPhone one time I had to use iTunes to restore the default system because there were a lot of applications installed on the phone already (which apparently increases the chances of a brick).
Is this the case with Android phones, specifically the Droid Incredible? I have been using it regularly for a period of two or more weeks and I would like to root it but I want to make sure it is safe to do so with a lot of applications already installed.