All My Apps Disappeared When Upgrading to iOS5

I upgraded my iPhone 3GS to iOS5. All my apps disappeared promptly. Here are instructions on restoring some of your apps:
In ITunes, on the left side select your iphone under "DEVICES" (I don't know why they shout at us in all caps).
Then on the horizontal menu bar across the top, select "Apps".
In the upper left corner of the window, select the "Sync Apps" checkbox.
In the app list below, check all the apps you want to restore.
Then in the bottom right select "Apply".

This reloaded all but my apps living in a subfolder. They are still missing. I'll update here if I can bring them back.