Before you allow any old program to just pop up and become the window with focus, check to make sure the user isn't typing something. Wait a few seconds before popping up. Not only is it frustrating, it could be a huge security problem. If I'm typing a document in word, and I need my credit card information or SSN, so I go to my secure app and copy it into the clipboard and go back to Word. Right before I paste and hit enter, some program that sends email to the world has figured out that it urgently needs to interrupt me for a comment, which it will immediately post to every blog on the planet, and my credit card goes out to the world.
It would be an easy thing to implement. The user could adjust the amount of time to wait before allowing a program to pop up, or you could also supply an option that would not allow other programs to pop up at all, but would instead keep them blinking in the task bar area until you click on them. Alternatively it could play a sound so you could stop typing, and the program would then pop up, now that the user is cognizant of it.