When you apply online for a job, often there is no option to include a cover letter. However, when you have the opportunity, you can customize your cover letter to match specifics listed in a job requisition. You can also bring up additional accomplishments that would be most desirable to each potential employer.
Cover letters are especially effective when you are mailing your resume. Hand write the envelope, put the words “personal and confidential” in the bottom lower corner, so your contact opens your correspondence.
In your cover letter, state WHY you've targeted their company, your level of interest and when you will be contacting them. When done right, cover letters DO enhance your job search.