[callydrias]

I've read through hundreds of online applications to hire a few people around here and here are my preferences:

Cover Letter
Put the cover letter in the body of the email. This is your foot in the door. Do not copy and paste it out of your Cover Letters for Dummies book, but instead, be a little creative. Keep it brief.

You want the person reading it to remember you - and believe me, there's rarely anything in a typical resume that will make you stand out. The cover letter is where it's at. One way to make the person remember you that you should avoid is to write and spell like a chinchilla. Proof read, spell check, and then have someone else proof read your letter. When spell checkers autocorrect words incorrectly, you look stupid.

Resume
Attach the resume as a separate document in whatever format is requested in the job posting (it almost always specifies). When in doubt, PDF is the best choice.

Try to keep it short, if possible. If it's multi-page, look at how it prints and make sure you don't have most of a blank page at the end. Leave room in the margin for the interviewer to write notes.

Emphasize your goals and major, relevant accomplishments. Leave out the details of that paper route you had in 7th grade or the pizza place you worked in high school (unless you have no other work experience or are applying to a newspaper or pizza joint).

Same spelling and grammar advice on the resume. I threw out at least 25% of applications because of poor written communication skills.

Good luck.