This happened to me when updating my first-generation iPad from iOS 4.3 to iOS 5. After installing the new software and unplugging the iPad from my PC, most of my apps were gone--along with all my music, photos, and other data. If the furious today is any indication, I'm not alone. Check a sample of the outrage:

Fortunately, you don't have to go back to the App Store to your apps back. iTunes should be able to restore those apps and any other lost data. Here's how:

If all else fails, you can click on the "Summary" tab under your device settings in iTunes, then click "restore." You'll see a dialog box that allows you to pick from a previous restore point. Choose a date prior to installing iOS5 (do not click "set up as new"). This will take you back to the way things were. Then, you can install iOS5 afresh.