I've finally installed Linux on my harddrive last week after all these years of procastinating and I now use it everyday.
I am pleased that Linux is proving to be a positive experience for you. Linux security is definitely a fascinating topic and in my opinion LQ is one of the premier sites regarding information on Linux security. Our focus, though, is on prevention, protection, and when the need arises a postmortem analysis of systems. Penetration testing is a gray area and the policy is to err on the side of caution to protect the reputation of LQ as an organization. While you may be using these tools for their legitimate purpose, LQ has no guarantee that this is how they will be used and the information could be used by someone else for nefarious purposes. My advice would be that if you need help with performing penetration testing on your systems that you consult the Backtrac documentation and forums. Then if your testing shows weaknesses that you would like help addressing, we would be more than happy to assist with the hardening process and actually be grateful for the educational opportunity.
As far as performing a scan of your system, be aware that Metasploit is very capable of "breaking things" in the process of performing its actions. You may be better off with a tool such as Nessus, Qualys, or OpenVAS, which aren't as aggressive and uses authentication to "open the door" as opposed to breaking it down.