Best practices for web application scanners

Tags:
Web application
Web application scanners
I was curious on best practices and standards for web application scanners as far as should our organization be looking for black, white or gray box solution? Also along those lines would commercial products such as Nessus, Qualys Web Application Scanner and/or FortifyOnDemand (HP product) be any that you would recommend for further investigation or do you have other favorite commercial WAS' products?


Software/Hardware used:
Nessus, Qualys WAS, Fortify-On-Demand (HP)
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