It's pretty simple. Just CD (or not) into the plugins directory (this directory location varies, depending on how you've installed it, but check /usr/local/nagios, or /usr/lib/nagios).
Find the plugin you want to run (if you're not sure, compare what you see in your plugins directory on your Linux box with the plugins located here: http://exchange.nagios.org/directory/Plugins, or try running "./plugin-name -h" to get the help info about the plugin).
The method for using any of these "plugins" from the command line is the same as any other Linux script: Just run "./plugin-name" with the appropriate flags you want to check, and viola!