Know Your Contact
Send it to the right person. An essential part of getting published is getting your query letter into the right hands at the magazine you want to write for. Many magazines publish writer's guidelines in books like The Writers Market 2002. Guidelines tell you what the magazine wants and who to get in touch with. The Writers Market is the freelancer's bible. It is a nice resource, containing contact information and other good stuff like pay rates for thousands of magazines.
However, don't be afraid to look elsewhere for guidelines. You can request them right from a publication itself and they can also be found on many Web sites -- but make sure the information is up-to-date. It never hurts to call a magazine just to ensure that so-and-so is still the senior articles editor, for example. Just don't try to pitch your idea over the phone.
If you don't have the patience to look for guidelines, simply get a copy of the magazine and address your proposal to the editor whose department you'd like to write for. This information can be found in the masthead, usually about 10 pages from the front of the magazine.