I just did the iOS6 upgrade, against my better judgement. Of course, after the upgrade it put my phone into recovery mode. I didn't think this would be a big deal because THIS time, I had backed up my apps.
Unfortunately, none of my apps are still on my phone. I have to re-install ALL of them. I don't even want to say how much money I sank into games and I'm cringing thinking that all of my progress has been lost.
My question is this: How do I get my back up if on iTunes, it looks like my apps are no longer even there!!!?
I had the same problem, but I just synced the iPhone to iTunes (using the cable), and all of my apps came back. They were all advanced a screen over from where they had been prior to the upgrade, so if it looks like they might not be there, keep going just to make sure.