We have had issues and it turned out to be high index fragmentation. We have a huge inventory so this was very impactful. This may not apply to you however, if you are running on a new DB. This can be resolved by defragging the indexes. Depending on the SQL server version you can do that without even bringing the table out of action.
Another tool to look at is DPA - you can run it on a trial basis to get information on that SQL instance. This is a bit of a heavy hitter, but if you are unable to find answers elsewhere, this one can often help.
If you have SAM as part of your environment, it has several templates that can assist with finding information about your SQL server and its performance.
The Microsoft forums are full of tips. But here are some additional ones from thwack and other sql sites. The usefulness will vary depending on your access to the system and comfort level running some of the queries.
