Unknown email at iOS upgrade
Is it possible that someone had access to your phone and/or your Apple ID? If someone tries to sign into iMessage using another email address (even without having your password) it will show up as an unverified alternate email in your Apple ID.

If they also added that email to your iPhone's Mail.app they could reply to the verification email while on your device. All they would need then is to get your Apple ID password and they would have a validated account on your Apple ID. Then you would have an "extra" email account linked to your ID, even if they deleted the accounts off of the iPhone when they were done.

Best thing to do is to check your account at http://appleid.apple.com, verify that there are no more unknown email addresses, then change your password!  Seriously! I saw this happen a lot when the upgrade from iOS 4 to iOS 5 first came out.