Thank you for a nice short explanation, PHeath! Following your advice, I found the best way to solve the problem is simply to use CATALINA_OPTS instead of JAVA_OPTS.
Looking into catalina.sh, one can see CATALINA_OPTS is only used by the "start" and "start-security" commands, whereas JAVA_OPTS is also used by the "stop" command (at least with Tomcat 6.0.33 on openSUSE 12.1).
At least if you have Tomcat installed on Linux using a package manager then modifying the CATALINA_OPTS variable in /etc/tomcat6/tomcat6.conf (or whatever path in your distribution) is cleaner than changing the catalina.sh script directly, for the package manager assumes that the user changes only configuration files and breaking this assumption may cause problems when upgrading the Tomcat packages (e. g. lost settings because the catalina.sh file is overwritten).
I think one should prefer CATALINA_OPTS over JAVA_OPTS not only for JDWP but for many other options as well: e. g. if one uses the heap size option -Xmx... then it would be reasonable to put it into CATALINA_OPTS, as the "stop" command does not need much heap.
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