I manage quite a few CentOS servers of the 4.x and 5.x versions. When I ran my yum updates this week I noticed that there was a Nagios update. When I restarted Nagios I saw that it had been upgraded to version 3. So far nothing broke because of the new version, but with the new version comes new features. You can read the changelog here.
NOTE: The beauty of Linux is that you don’t have to restart your system when you install updates (except for the kernel). But if the package manager (yum, apt, etc.) doesn’t restart the service the old binaries will still be running. So for example when I installed the Nagios update today version 2.x was still running so I had to restart Nagios to actually be running 3.x (command: service nagios restart).