Most company policies require the messenger service to be disabled.
I believe any form of net send - either CLI or via Server Manager tools utilize the same service/protocol for this communication.
There are 3rd party tools to accomplish what you're after, but if you're looking for something native/free, then you might try using the shutdown tool. In a real emergency, you aren't going to care if the system is actually shutting down or not. However for those 'lighter' emergencies, you will still get the benefit of having priority over all other desktop processes as this message appears in the foreground.
There are multiple methods of delivering such a command to your clients, parsing through a text file is one way.
But essentially you would run the following against the targeted machines (from an "Admin" console):
shutdown -m \\Computer -s -t 900 -c "Building is on FIRE!! Evacuate Immediately!"
This gives you a 15 minute timer (increment the -t "seconds" as desired).
If it's any less of an emergency, you could still use this feature, but obviously you're scaring the pants off your employees as it does indicate the machine is shutting down (top box). Your comment(s) appear in the bottom box. You can test it out yourself, you would just run
shutdown -m \\Computer -a
to abort the procedure...
