I would use sp_whoisactive (AWESOME freebie found on sqlblog.com) to see real-time query execution metrics (including query plans). I would also use profiler to capture simple execution metrics and use Qure from DBSophic (another AWESOME freebie) to do aggregate execution analysis. Often the query(s) you REALLY need to tune aren't the ones that run for 5 minutes. They are the ones that run for 1 second but get called 10 times per second.