It bothers me that many writers don't know the difference between a cover letter and a query letter, and I keep seeing the same misinformation posted in open forums. So, here's my Rant of the Day:
If you include a letter with a manuscript, it isn't a query letter, it's a cover letter.
A query letter is what you send asking an editor if she wants to see your manuscript.
The essential difference between the two is that the query letter is a sales tool and the cover letter is an informational tool. That is, the goal of a query letter is to make your manuscript seem so appealing and so perfectly targeted that an editor asks to see your manuscript. A cover letter is intended to provide some potentially important or useful information about yourself or your manuscript that isn't obvious from looking at the manuscript alone. If the manuscript's enclosed, it had better sell itself.