I'd like to know the standard way to benchmark a SQL Sever Query, preferably I'd like to know about the tools that come with SQL Server rather than 3rd Party tools.
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set showplan_text on will show you the execution plan (to see it graphically use CTRL + K (sql 2000) or CTRL + M (sql 2005 +)
set statistics IO on will show you the reads
set statistics time on will show you the elapsed time
+1 on the execution plan. From here you can see where all the time is being spent in your particular query. Eg. 85% of the time is spent table scanning a particular table, can you put an index on that table to improve it? etc etc.
Use SQL Profiler.
For .NET applications, filter that Application name by '.NET%' and you'll omit other extraneous queries.