I don't have a iPhone but a iPod Touch but I notice with the apps I run I still get annoying pop-ups disturbing when using them. For example I opened TuneIn Radio and a stupid pop-up came up telling me to rate the app. I already rated the app yet it still pop-ups. I have to click No Thanks before I can use the app. I thought Notifications would show a message on the top of the screen that you can just ignore. This is not the only app giving me pop-ups. By the way the first thing I did after installing iOS 5 was to go into the settings and changed all of the notifications to the banner mode but it does not make a difference.