After you have a clear idea what you will assess, you will choose a set of tools to do some of the job for you.
I would suggest nessus, that is good one (although a pain in the neck to install without linux expertise)
It has a client-server archicture, well documented and (usually) up-to-date to vulnerabilities
http://www.nessus.org/

People that passed the nightmare installation phase really like to tool.