Many websites and processes tend to require some sort of notification for the user from errors, to processes completing, to even an overall important alert for a campus or organization that needs to be recognized when the user visits a site.
Here are a few of the notification systems we like to use:
1. JoliCode - Desktop notifications for systems (not typically web) - A really great library of notifications that attempts to do it's best job at delivering it based on your operating system but has a Drupal module.
2. Chrome Notifications - Been seeing those notifications that every website would like to send you notifications now on Chrome browser? This is how to do that with Drupal nodes!
3. Using goRoost! - You can send notifications through this third party service
4. Using WebSignal - Another great third party to plugin to post alerts.
If you're looking more for like a campus alert system that's hosted off-site you could also take a look at perhaps http://www.e2campus.com/
Some modules we have used in the past include: