&snip;
Once we know that the JDK/servlet container work on FreeBSD (which is an open question), we can continue the conversation as to how to integrate it with the cocoon.apache.org site. I'd prefer using mod_jk2 (if using Tomcat - or if using Jetty its connector - it has one, right?) over a ProxyPass connection, but let's cross that bridge when we get to it.
What version of BSD is running? I've had problems with the JDK and slightly older versions of FreeBSD, where Java would only run as root (!), and it was a documented bug in the FreeBSD kernel... it was pretty nasty AFAIR. I hear they've fixed the problem in the latest releases (4.8-R, etc), but I wouldn't be 100% on anything older than 4.8 or 4.7-R.
Tony