When you have Restored you iPhone, all of your applications will have to be installed again, one by one. This is a lengthy process, since each application could take a mean time of around a minute to install. That is, if you had 500 applications on your iPhone, it could easily take up to 8 hours for all of them to finish installing!
Do not try to use an application that has not installed yet (it's icon is grayed-out), keep tapping on grayed-out icons or fiddling with the App Store, you won't accomplish anything, you'll just end up pausing installs.
Let your iPhone finish its thing on its own pace. All applications will eventually install. You do NOT have to put the iPhone aside as long as the applications are installing. You CAN use your iPhone normally, at least with the applications that have finished installing.