I am adding to the server a tool to monitor system resources a bit closer and will try Munin first. Installation is described at http://www.howtoforge.com/server_monitoring_with_munin_monit_debian_etch, the tool is described at http://munin-monitoring.org/
Just to avoid this in future … there are two very detailed descriptions on how to setup and prepare the installation of a SSL certificate for Glassfish3. Just one of them creates a mess and makes the server un-starteable. So, the correct version is: http://kalali.me/how-to-prepare-for-and-install-godaddy-ssl-certificate-into-glassfish-v3/.
And just to complete the topic: this is the best way to deal with all keystore issues: http://weblogs.java.net/blog/2007/11/19/ssl-and-crl-checking-glassfish-v2#4.
Well, I hope I am ok with those certificates for now.