Please, if you're submitting manuscripts to a magazine or publisher, do the slush reader and yourself a favour. Be professional. Your chances at actually getting a story passed on to the editor will increase dramatically. Show me that you're serious about getting your work published. In the submission form, there will be a section for a cover letter. Write something here. Put in a short summary of your story, as well as any relevant qualifications that you may have. If you can't bother to write anything here, why should I expect your story to be interesting?
Your goal is to make it easy for me, the slush reader, to enjoy your story. Asking me to google your name in order to find your publications is not going to earn you any points. Frankly, I'm busy. I'm not going to bother doing this, and I'm going to just pretend that you have no relevant qualifications. For all I know, this may be true. You certainly didn't point anything out as being especially important. I probably won't follow a link to your website for your qualifications, unless there's something really interesting in your cover letter. I have enough tabs open in my browser right now. I don't really want to open another. What is best here is to provide a short list of your relevant publication history. If the market is smaller, and not necessarily related to the current market, it might help to explain what it is. Is it a small university literary journal? Or is it a flash fiction online journal? Paid markets are likely more relevant.
Most importantly, if you have ever been accepted at my market, mention it here. If you have received personal feedback from the editors here, mention it. Do not assume that I'm the slush reader who read your last story. Do not assume that the editors will immediately recognize your name. If I'm not made aware of any past acceptance or feedback from the editors, I'm going to treat your story like all others. If I know about prior feedback, I'll still read it and provide comments to the editors, but it will be passed on to them for further review.
Now to the manuscript. For the love of all that is pure and good in this world, do not use the Papyrus or Comic Sans fonts. There is something to be said about a good non-proportional font like Courier. The Van Halen brown M&Ms contract clause is a true urban legend. Paying attention to the small details will show that you're serious. There are numerous manuscript guidelines available online. Here's a link to Science Fiction writer Robert J. Sawyer's manuscript checklist. Ignoring this advice won't make me reject your manuscript, but following it will help.
As for the manuscript's content, how many times have you read it? Have you read it aloud? Where does it trip you up while reading? Sometimes it can help if you read it in a different voice. How would James Earl Jones narrate your story? How would William Shatner narrate it? Remember that although his reading of Sarah Palin's rejection speech sounded poetic, doesn't mean that the original material was very good.
Try to remember that with electronic submissions, the words you see underlined in red in your word processor appear underlined in mine as well. Don't draw attention to problems in your manuscript. Do you have a part in your story where you have several paragraphs of backstory? This is called exposition, and it will kill my desire to read any further. This is even worse when the exposition is more interesting than the rest of your story. If you really feel this information is important, break it up into smaller chunks to be revealed slowly throughout your story. Keep me interested in your story.
Pay attention to the mechanics of narration. Don't suddenly shift verb tenses, or point of view. The traditional modern story is told in third person, using the past tense. "He picked up the gun", not "I pick up the gun" or "He picks up the gun". Unless you have experience writing in other forms, try and stick with the standards. Remember, your goal is to make it easy for me to pass your story on to the editor.
In general, be professional and courteous. Give me context in your cover letter, and make it as easy as possible for me to like your story. I will appreciate it.
For a similar perspective on submissions, read Molly Tanzer's post from higher up on the slush pile.