There were older, desktop apps that made modal dialogs appear that blocked you from doing anything if you had an update, message, whatever. I later saw that turn into a dedicated box with significant chunk of screen. At least I could do other things. Later, there was a menu or window somewhere that could be opened with the notifications being smaller instead of the message itself. Later, on Xbox Live, they made the notifications pop up in top-center of screen with very little info in them. They also let me turn them off with a one-button method of checking if anything happened in-game. A further enhancement of this might be replacing the popup with a distinct, mellow, sound effect that blends into in-game sounds in such a way to stand out but not jolt a person out of the game. Not just preserving the mood of one but also not say masking sound of enemy footsteps.
So, in just that one area, things have improved remarkably from the time when developers said, "We're going to shove this in their faces and force them to pay attention." I'd love to see more such improvements across the board leading to calmer software.