Not all "pop ups" are bad

Email notification with subject is probably counted as a pop- up i know Thunderbird looks a bit like a pop-up, not used Outlook for a while but its probably similar.

Text message notification on a mobile, on my HTC it shows a picture in the top bar and get my attention when im doing something else.

This (and many other) patent is crap , its like saying you can't raise your voice to get somones attention when they are involved in another activity.