I know that policy auditor can check for Microsoft Patches as well as many other OS patches, but can it check for vulnerable applications like java, flash, adobe, etc on Windows. In a mobile environment a standard scanner can catch mobile devices so I was hoping to find out if these apllication checks are provided in Policy Auditor before spending too much time researching. Any info would be appreciated.
Yes, it can do pretty much anything you need. There are also lots of checks that come packaged with it and there are various sources that have downloadable content. Note PA imports XCCDF format benchmarks or you can create your own custom audits.
Here's a link to a public site example that provides importable benchmark checks:
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