So I tested out Skipfish today to do a quick check on a website / web server. Hosted on Google at: http://code.google.com/p/skipfish/ download it, extract it and make and run:
wget http://skipfish.googlecode.com/files/skipfish-2.01b.tgz tar xzf skipfish-2.01b.tgz cd skipfish* cp ./dictionaries/medium.wl . make ./skipfish -o ./myreport http://domain.co.uk/index.php
Skipfish will create an HTML report in the ./myreport directory in the file index.html
For more info read the well written README files in the tarball.
Another useful tool in addition to OpenVAS (Nessus) and one which could be scripted to provide a web interface – added to the TO DO list!