Yeah, like the last person said it's faster to reinstall. Plus if you've got any large apps, remember that downloading them again will eat into your monthly allowance on your phone plan.
Also, some apps are pulled from the app store [for various reasons]. VLC player was pulled because of a rights dispute, so I doubt you can re-download it from the cloud, and NBA Elite '11 and a few other games were pulled [presumably] because their license expired [not sure if they are still in the cloud]. My advice would be that if you really do need to delete them from iTunes, back them up to an external first so that you can always re-install if you need to.