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When you are hired as a DBA in a new shop, what are the important tools that you would use for establishing baselines and implementing benchmarks for 50+ instances? You advice would be highly appreciated.

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For Microsoft SQL Server, the lowest-intrusive tool is Performance Monitor, aka Perfmon. Here's my tutorial on grabbing Perfmon counters for SQL Server and analyzing them:

http://www.brentozar.com/archive/2006/12/dba-101-using-perfmon-for-sql-performance-tuning/

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