The Journalist's Toolbox has some nice references on applying for jobs in the writing world, so I rounded up a few for you?

Basics on the cover letter. I'm not totally sure what it means to avoid the form letter, but I will say this: If you are using a form letter, MAKE SURE YOU HAVE THE RIGHT NAMES ON THE LETTER. Don't apply for a job at USA Today and say in the body that it's always been your dream to work for the Times

Here are some examples of good cover letters.

How to package it all up. I wouldn't stress about this too much as long as everything looks neat and professional.