When nVidia released their 'beta' drivers for Win8 RP (302.80), I installed that version but had some problems with it. Still, I kept it for a couple more days. Then, I decided to downgrade to a less buggy, Win7 driver. That's when the 1st party metro apps just stopped working (I tried opening them, but they would sit at the loading screen for a couple of seconds, then they would trow me back to the Start Screen). I assumed it was because of the video driver so I reinstalled the 302.80 driver. Still, I experienced some problems and now not even the 3rd party apps would run. Just now I installed the 302.82 version of the driver, the WHQL certified one. It doesn't seem to have solved the issue either.
Oddly enough, Fruit Ninja works just fine.
Should I "Refresh My PC" ? Should I just wait and hope they'll just start working again?
Also, I seems I can't change which apps notify me and which don't. The items related to this option are simply not showing up in the Notifications area of the Metro Control Panel.
Maybe the solution is just in front of me and I'm too stupid to see it?
Uninstall all your apps and reboot your machine. Once back up and running, go into the Store, right-click, select Your Apps. Then select the apps you want to reinstall, I'd start off with the first party apps.
Once you've reinstalled them they should be working again.
For individual app notifications, try selecting from within the app itself. While in the app pull up Charms>Settings>Permissions... this is where you should see the option to turn on notifications for most apps.