In my case, I have more apps in the Sync Apps list in iTunes that are no longer installed (unchecked) than those that are, making it a chore to sort and manage the apps on my iPhone and iPad.

This is good if you might one day want to redownload it, but it creates a rather lengthy and unmanageable list when you go to sync your phone. The problem is that if you delete an app from your iDevice, the app remains listed in iTunes. Granted, I download more apps as a tech writer than the typical iDevice user, but if you've had an iDevice for more than a few months, however, it's likely you have deleted many needless apps and free trials after trying them out.