I have created an application that runs in the taskbar. When a user clicks the application it pops up etc. What I would like is similar functionality to that in MSN when one
There's support for notification balloons in Win32 (I'm not a .net programmer), with some useful properties as old new thing explains.
There's also a system wide semaphor which you should lock to prevent more than one popup from any application appearing at once.
There's a a couple of pages on the toast semaphor on msdn - the toast semaphor and in the broader context of usability. I also came across some example code to use the balloon api from C# while looking, but can't vouch for it.