Lynis is Unix based software and its free under the GPL and a popular security hardening solution. The advantage here is that it does not change any of your configuration files. Instead, it lists what it seas as weak or needs to change. It can scan your system in details and very extensively. Its use is straight forward, and it is OS independent, which means it will run in almost any Linux or Unix environment. You can run Lynis from USB, Cd, ext. HDD or any other media.
With proper plugins, Lynis can test your databases, e-mail servers, web and what not. There are many documentations and video presentation regarding installing and configuring as well as using Lynis. I advice you to search for these and read as much as you can until you feel comfortable and start testing and using it.
Latest version of Lynis as of now is 2.1.0 and can be obtained at: