CATALINA_OPTS v JAVA_OPTS - What is the difference?

There are two environment variables - CATALINA_OPTS and JAVA_OPTS - which are both used in the catalina.sh startup and shutdown script for Tomcat. They are described in comments within that file as:
(optional)[color=red] [b]Java runtime options used when the "start", "stop" or "run" command is executed [/b][/color][JAVA_OPTS]
and
(optional)[color=red] [b]Java runtime options used when the "start" or "run" command is executed [/b][/color][CATALINA_OPTS]

So why are there two different variables? And what's the difference?

Firstly, anything specified in EITHER variable is passed, identically, to the command that starts up Tomcat - the "start" or "run" command - but only values set in JAVA_OPTS are passed to the "stop" command. That probably doesn't make any difference to how Tomcat runs in practise as it only effects the end of a run, not the start.

The second difference is more subtle. Other applications may also use JAVA_OPTS, but only Tomcat will use CATALINA_OPTS. So if you're setting environment variables for use only by Tomcat, you'll be best advised to use CATALINA_OPTS, whereas if you're setting environment variables to be used by other java applications as well, such as by JBoss, you should put your settings in JAVA_OPTS