Retina by eEye is awesome, but not free (trial with limitations).
I've used nessus, and I'm not sure it's as comprehensive as eEye, but I've only used it on my own machine. eEye makes nice reports for your boss, I hear.

Nmap, thehorse's tutorial are wonderful. Make sure you know what your users have access to, make sure you can respond properly to any breach or scenario.