Pay attention to job site’s application specifications about whether the resume can be sent as a word document or pdf. Make sure you are sending the format they want!
Proof read your resume. Use but do not rely on “spell check”. Print it out for a final check.
Include the title of the position you are applying for in the subject line of the message. It streamlines the process of figuring out the purpose of the e-mail and thus increases its chances of getting through to someone who can actually hire you.
Be sure that your email address/screen name has a professional tone.
Challenges to Apply for a Job through a Company's Website
Many companies are adopting software known by the generic name “Applicant Tracking Systems” or ATS. Companies do not have the manpower to go through all the job applications they are receiving. This can complicate the life of the job applicant.
The following is a link the a more detailed article about the APT.