Preventing iPhone 3GS from auto-updating to iOS 6
Fortunately for you, iOS will not update without your consent. You have to physically go in and choose to Download, and Install the Update (two steps) in order for it to update to the next version of iOS.

iOS 5 or higher have a feature called OTA (Over the Air) updates, which bring the convenience of not having to plug your iPhone into iTunes to update it - which you are aware of. It displays a badge on the Settings app on iPhone homescreen, but this will still not update without your consent (unlike some Windows OS updates).

Unfortunately, the Settings.app is not in the list of notifications that you have control.  So you will have to get used to seeing the "1" on the Settings.app.

You will also have to be careful to decline (skip) updating your device anytime you plug it in via USB to iTunes. One thing to note, is that you don't have to worry about Wifi syncing with your device. It will not update your device using iTunes Wifi sync.