Nessus review by PC Magazine: "Based on a client/server architecture, Nessus lets users run the administrative console, which executes vulnerability scans and holds databases on a machine other than the ser".
I personally think PC Magazine was dismissive of Nessus. These magazines tend to be biased against the non-Windows platforms. I have not done so myself but one can write one's own security scans via the Nessus plug-in language (NASL) and there is at least on Perl module available to programmatically control Nessus. My employer has built a Linux, Apache, PostgreSQL, and Perl based vulnerability assessment application around the Nessus security scanner.
Fyodor, the developer NMAP, the open source port scanner, announced the release of version 3.50. NMAP, or network mapper, is a software utility for security auditing and exploration. This release adds some important and exciting features and takes the software in a new development direction. Some of the features and enhancements are:
Advanced service/version detection system.
Improved operating system detection process.
Better formatting of output.
New fingerprint classification system.
In response to SCO's lawsuits and claims of infringement against Linux, Fyodor has taken an unusual stance by terminating SCO's license to NMAP on all of SCO platforms. A risky move but then that's Fyodor.