There's certain value in performing basic checklist audits on your systems. Various security standards from The Center for Internet Security and the National Institute of Standards and Technology can point you in the right direction. Using an audit checklist during a security assessment will help you validate that certain controls exist. The problem is, you won't know which vulnerabilities can actually be exploited. It's this exploitation component you should focus on; you've got to look at the entire picture.
Similarly, with automated vulnerability scanning tools, you may find missing patches and misconfigurations, but that's not the entire picture. I write often on the importance of using good tools to find security vulnerabilities. I strongly believe we can't live without them. The problem is it's easy to stop at automated vulnerability scans assuming they're omniscient. This is not true.
Without manual checks through the eyes of a malicious user or external attacker, we won't know which vulnerabilities can actually be exploited in the context of our networks. We also won't be able to see other usability-centric flaws that no tool would ever find.
Security assessments and five mistakes to avoid
Step 1: Relying on audit checklists and automated tools
Step 2: Not considering the side effects of your tests
Step 3: Not looking at the whole picture
Step 4: Spending too much time trying to fix everything
Step 5: Assuming testing once is enough
About the author: Kevin Beaver is an independent information security consultant, speaker and expert witness with Atlanta-based Principle Logic LLC. He has more than 19 years of experience in IT and specializes in performing information security assessments revolving around compliance and IT governance. Kevin has authored/co-authored six books on information security including Hacking For Dummies and Hacking Wireless Networks For Dummies (Wiley) as well asThe Practical Guide to HIPAA Privacy and Security Compliance (Auerbach). He's also the creator of the Security On Wheelsaudiobook series. You can reach Kevin at firstname.lastname@example.org>.