IOS – 3Gs after 5.0.1 upgrade, all third-party apps can not open and work

I tried jailbreaking and installing iOS 4.2, and the issue persisted so I concluded it's a hardware problem. After four months, I finally got the battery replaced, and the service guys told me there was a problem with the old battery's circuit.

The new battery works just fine.

When I first updated to iOS5 I lost all of my apps too. Interestingly, it had the spinning sync icon at the top of the phone for a few hours after as it manually downloaded all of the apps. They suddenly appeared one after another. Perhaps it's doing this.

Try downloading an app that you had and see if it still has the settings/saves it had. If so, I'd expect this is the case.