I think a modern operating system needs to include a standard notifications service that any program can link into. I think that's one of the subtle things Android (and other phone operating systems, in their own way) have done right. There is a separate area at the top of the screen (while in the main launcher) that is only ever used for notifications. They do not pop up over anything else, they never need to steal space from anywhere, and you always know where to look for them. Compare that with Windows where there's an expanding area at the bottom-right corner of the screen, and it can pop up balloons over what you're working on. That's the unobtrusive version. A lot of the time applications have their own focus-stealing popup windows that just don't
Maybe this is more a discussion to have about modern GUI frameworks rather than operating systems. They're often tied closely together, though. Also, a GUI framework can't reserve space on the screen except in its own window, right? So a notifications area needs to be a feature of the OS window manager.
I guess phones have a bit of an advantage with a different kind of app structure than Windows. Apps are expected to be one-at-a-time and full screen, which forces the notifications area to be what it is. Windows, being built on legacy expectations, having more power and freedom for applications than a mobile phone, allows actions that can be very disruptive to the user's workflow.
Mokalus of Borg
PS - There are lots of ways to do notifications right.
PPS - Windows doesn't do any of them.