Free Security Assessment Tools

Security System Analyzer :
OVAL-compatible product
Fully support of open security standards and initiatives (CVE, OVAL, CCE, CPE, CWE, CAPEC, CVSS, CRF)
Perform a deep inventory audit on installed software and applications
Scan and map vulnerabilities using non-intrusive techniques based on schemas
Detect and identify missed patches and hotfixes
Define a patch management deployment strategy using CVSS scores

http://www.security-database.com/ssa.php

MS Baseline Security Analyzer:
Vulnerability assessment scan tool for MS products

http://technet.microsoft.com/en-us/security/cc184924.aspx

Secunia Personal Software Inspector:

Scan all the software installed on your PC, and advise you to update un-patched software.
http://secunia.com/vulnerability_scanning/personal/


Microsoft Security Assessment Tool:

MSAT consists of over 200 questions covering infrastructure, applications, operations, and people.
The questions and the recommendations that the tool offers are based on standards such as ISO 17799 and NIST-800.x, MS trustworth computing group and other external resources.
http://technet.microsoft.com/en-us/security/cc185712.aspx

Application Pen-Testing time Estimator:

http://www.coffeeandsecurity.com/resources/tools/tamapper.aspx