Working as an assistant in a Human Resources department and as a superviser hiring student interns, I know how little time employers spend looking at résumés. Résumés are definitely important, but they are used in the quick sorting process to answer the question: "Does this person have the necessary skills and work experience?"
The cover letter has the meat (or for vegetarians, the "tofu") of the information that helps the employer get a better picture of your qualifications.
Lifehacker recently posted an article titled, "How to Write a Cover Letter That Employers Will Actually Read." This article provides a great overview of key things you can do to make your cover letter stand out from all of the other applicants.
The most important tip is to never use the same cover letter twice. It can be time-consuming to write a different cover letter for every job you apply to, but it is a necessity. The reason you need to write different cover letters is that you need to match your skills and qualifications to the job requirements. You need to use the keywords and buzzwords that the company uses and show the skills you have that the company wants. No one wants to read a generic "here are my accomplishments" cover letter because it is hard for the employer to figure out whether your accomplishments will transfer over to the job. Read the Lifehacker article for more helpful tips.
To learn more about writing cover letters, visit these websites: