I've found a great tool in a blog of an employee of Microsoft Israel named
The tool overview (from MS site)
The BizTalk Server 2006 Best Practices Analyzer performs configuration-level verification by reading and reporting only. The Best Practices Analyzer gathers data from different information sources, such as Windows Management Instrumentation (WMI) classes, SQL Server databases, and registry entries. The Best Practices Analyzer uses the data to evaluate the deployment configuration. The Best Practices Analyzer does not modify any system settings, and is not a self-tuning tool.
The blog post located here:http://blogs.microsoft.co.il/blogs/adlaim/archive/2008/04/14/biztalk-best-practice-analyzer-v1-1-rtm.aspx
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