I have enabled notifications on gitter (for a project I'm a maintainer of) when I'm directly mentioned. That's a legit use-case.
But pretty much every other prompt has been obnoxious.
A friend and I made www.timetaco.com, which gives you a countdown to an event you specify, and can send you a notification a few minutes earlier. I think that's one of the few legit use cases I've seen.