Rooting a regularly used Droid Incredible
Rooting won't affect any applications that are already installed.  All you're doing is giving yourself administrator rights to your phone.  You won't have to wipe/reload, etc. unless you plan on installing a custom rom.  If you do want to install a custom rom, I highly recommend using Titanium Backup to backup all of your apps and their data.  Also do a Nandroid backup (it's like making an image of your phone that you can restore to) right after you root and before you do anything major to your phone (such as installing a rom).