When all of the settings have been restored to the iPhone, it will restart again. You'll see it disappear from your iTunes window, and then reappear again.
If you have iTunes set to sync automatically when the iPhone is connected, the sync will begin now. If you don't have it set to sync automatically, you'll want to start the sync manually now.
The first sync can take several minutes, as this is when all of your files, including your apps, music, and videos, will be transferred back to your phone.