A cover letter is sent along with a resume to highlight how the accomplishments listed on your resume are relevant to the needs of the recipient. If your reader picked up your resume, would s/he immediately see a connection to the position? If the answer is no, think of the cover letter as your opportunity to make that connection.
The cover letter typically serves as an introduction, establishes for the reader what position (or assistance) you are seeking and hopefully entices them to read your resume. It is generally no more than one page in length. The cover letter should clearly describe your interest in the role -- why are you applying? The letter should also highlight your relevant skills and experiences in regards to the position that you are seeking. Finally, it is also your opportunity to present relevant qualifications that may not be on your resume.
Traditionally, a cover letter was written as a formal business letter with the resume as an enclosure. E-mail has changed the way cover letters are used and delivered. When submitting a resume via email, the body of the e-mail could serve as the cover letter. Brevity is essential in an e-mail. Alternatively the cover letter and resume may be submitted as one file (a .pdf file will ensure that format is not compromised) included as an attachment to an e-mail.