I need a good vulnerability auditing tool for Ubuntu so I decided to try nmap I also recalled that there was a product that can do this kind of work called Nessus it is no longer available in the repository and the packages for Ubuntu at its site http://nessus.org/nessus/ are old, I suppose that the latest one may work on maverick though, does anyone have any experience using nessus? How does it compare to nmap?
As far as I'm aware, Nessus is no longer free. You should take a look at OpenVAS, which is a Nessus alternative (and has even better coverage), instead.
OpenVAS (Nessus alternative) and Nmap are very much different. You can use OpenVas to find vulnerabilities without knowing how to look for them as OpenVAS tries out numerous attacks collected from various sources, whereas you do need to know what you are doing, where to look for, with Nmap.
You can still get Nessus for Linux. You need to download it direct from http://nessus.org/nessus/
Please note that there are differences between the pay for version and the free version. See here -> http://nessus.org/documentation/index.php?doc=faq#anchor66
Nessus is available in a Free version (non-commercial use only).
OpenVAS the fork of Nessus is Open Source and continues to be developed (http://www.openvas.org).
NexPose is a vulnerability scanner from Rapid7, community version can scan up to 32 IP's for Free.
Nmap with NSE can perform vulnerability checks (as mentioned above).
A comparison was done recently between the different scanners - http://hackertarget.com/nessus-openvas-nexpose-vs-metasploitable/