What works for me is to only update through the App Store on my iPhone. I had this problem big time with my iPod touch 1G that only went up to iOS 3. Now I have an iPhone 3GS that stops at iOS6 like yours.
If you look at the updates available on the phone, you will only see the ones that will work on the iOS version on the phone. Not the best solution, but it works.
Where it does not work if when you g3et an update that is supposed to work on your iOS verison but crashes all the time. I have one of those (and a couple where the update is junk and ruins the app) so I downgraded to an earlier version. And, of course, the App Store in the phone keeps nagging me to update, so I have to ignore those updates.
It would be nice if Apple would add a feature to iTunes so you could set it to ignore certain updates, but I'm not holding my breath.