http://www.simple-talk.com/sql/performance/finding-the-causes-of-poor-performance-in-sql-server,-part-1/

http://www.simple-talk.com/sql/performance/finding-the-causes-of-poor-performance-in-sql-server,-part-2/

Missing index DMV = suggestions, not directives. If you're looking at a long-running query, you can use that to see what indexes SQL thinks is missing on the relevant tables. Just creating indexes from it blindly will likely give you far too many, far too wide indexes.

p.s. A 3 minute filter's too long. What about the 10 second query that runs 120 times a minute? Is that acceptable, but the 180 second query that runs once an hour not? Is 2 minutes 50 seconds OK and 3 minutes 10 too long? Default application timeout is 30 second.