A few places to start with troubleshooting.

- Check for blocking in sys.sysprocesses or sys.dm_exec_requests

- launch perfmon and look at Avg. Disk Queue Length.

Dont pay attention to size of number (calculating your ideal range can vary based on disk e.g. SAN vs Local vs # of drives), but you can at least see what the numbers are when the server is running normal. Then see what the values are when the query runs good vs when the query runs slow. Basically get your baseline and compare.

-Size of Results returned. If large amounts of data is returned to web browser it can take time for the application and browser to render the results

-check sys.dm_exec_requests and see what the wait type is. Most likely it will be IO related, but you may get surprised.