If you do not have any backup, you may not be able to have them "as they were" per se, but you can redownload all of your apps from the App store by going to Updates > Purchased > Not on this Phone, or through iTunes on your Mac or PC by going into the iPhone menu (when it's connected to the computer) and clicking the Apps tab at the top. You can then check the apps you need to sync over.
When you restored, you should have been given the option to restore from a backup - that's how you would normally keep your settings and whatnot, otherwise it goes back to Factory settings. If you didn't restore from a backup, I would recommend restoring again, and selcting the most recent back up from the menu that pops up.
Yes, that's exactly what I did. I was give the option to restore from the backup I had done 10 minutes earlier. I am hesitatnt to restore again from the most recent backup since I have it set to wirelessly backup and it may have updated to the current condition with the missing apps since then.
All of my purchased apps are downloaded into iTunes. And I obviously did the restore via USB. Everything should have been copied back exactly the way it exited before I did the restore as I understand it.
If I ran a point update on OSX for my desktop mac, and it wiped down all my apps *and* my files... do you know how ****** off I'd be?
Why doesn't iTunes rip down all your apps & data, and then push them back when it's all finished updating? Have to say I'm highly unimpressed by this hidden feature of uninstalling everything and wiping your app data. Have lost critical data. Why? Because there is a radio button option to back up to iCloud *or* your desktop computer? I had it set to iCloud.
Not like it's easy to get into your iphone's data stores and back up your data manually, either!!