A cover letter is different than the resume. Your resume is a list of data and concrete information. Your cover letter allows you to integrate, synthesize, and energize your application. It can go beyond what is on the resume and showcase your writing ability. Warning: Not all jobs require you to submit a cover letter.
Use a traditional business letter format and heading/font/layout that matches your resume.
For more information and examples visit: http://owl.english.purdue.edu/owl/section/6/22/