Oh, God, where do I begin?
The apps listed for updates in iTunes and the phone are always completely different, and using either to actually do an update doesn't work at all! I usually have to delete a program from the phone *and* iTunes and download it over again to get an update. And even then it doesn't always work.
I can't imagine what would happen if my hard drive were to die so that I couldn't delete my apps with iTunes anymore.. It would be either reformat my phone or stick with old app versions!