Wirelessly posted (Mozilla/5.0 (iPhone; U; CPU iPhone OS 4_2_1 like Mac OS X; en-us) AppleWebKit/533.17.9 (KHTML, like Gecko) Version/5.0.2 Mobile/8C148 Safari/6533.18.5)
Last time I restored, the backup remembered my app folders, etc.
It's possible the backup will also include the apps without one having to manually select. However, I don't know if that's the case for apps deleted on the sync computer.