"Leave it on" is an app that has several features in which one is a very well designed sms/email popup. It can also be setup where the popup does not happen if you are already in the sms app.
I use BerryPopup, and you can set it to not pop up in specific apps. Both BerryPopup and Leave it On have free trials, so try them both and see if you like either one.
Posted from my CrackBerry at wapforums.crackberry.com