All of our submissions are electronic, so some of my issues are specifically related to that submission style, but many of them apply to the postal style, too.
The first thing I want to say is that Standard Manuscript Format matters to me. It matters a lot. It matters enough that I capitalized all three words of it, and linked to the easiest and best example of it to be found online. Standard Manuscript Format is an easy-to-read way of presenting a story that makes life much nicer for the people who read hundreds of submissions. I'm never surprised when new writers don't use it when they send in their stories, but I find it kind of shocking when experienced, published writers don't. It isn't just a stupid rule you have to follow when you're starting out; it's a courtesy. Making your submission as easy to read as possible is a way of being kind to the people who are doing the reading. It also makes you look better, and more professional. Even if you hate the way Courier New looks on your screen, you can compose in whatever font you like and then change it for the final version that you're going to send out.
Another thing to consider, if you want to look really polished, is the file name of the document you're going to send. Let's say your name is Farvel Manuscriptor and your story is called "The Seventeen Half-Dogs of Wachilia." Here are some possible file names for your final, submitted story that you're sending to Clarkesworld:
A. Manuscriptor - Seventeen Half-Dogs.doc
B. The Seventeen Half-Dogs of Wachilia.doc
C. The Twelve Half-Dogs of Wachilia - draft three.doc
D. Manuscriptor - Seventeen Half-Dogs - WotF Version.doc
Do you see how A and B are more professional-looking than C and D? No? Here's what looks a little funny about C. Everybody knows that writers write multiple drafts of stories. It's just a little weird to send in a rough-drafty file name, with a draft number and a different title than the final one that appears in the manuscript. Then there's D: why would you ever need to leave in the name of the other market that has already seen and rejected your story?
A little thing like a weird file name isn't going to get your submission rejected, but the little details add up toward the reader having a positive, or a negative, first impression of your work. Which would you prefer?
Two more things remain on my list. Cover letter, and title.
I'm sure there are a lot of different opinions about cover letters, and I'm sure that not everyone will agree with mine. You don't have to. Again, it won't be a deal-breaker no matter what you send, because the story is the main thing. Just let it be known that I like a minimal cover letter. For an aspiring writer, my ideal cover letter for the story above would be the following:
Dear Neil Clarke,
Please consider my previously-unpublished story, "The Seventeen Half-Dogs of Wachilia," for publication in Clarkesworld Magazine. It's about 3,000 words long.
Thank you for your time and consideration.
From a previously-published writer, it's nice to see a short paragraph in the middle with the best three markets where their work has appeared, along the lines of, "My stories have appeared in Weird Tales, Fantasy Magazine, and Electric Velocipede," or a mention of which novels you've had published most recently. There's no need to paste in your entire publishing history. Extra information doesn't help.
There are some variations that work just fine, too. If you want to be more formal, send the note to Mr. Clarke. If you've met him at a convention and feel comfortable, send it to Neil. If you want to acknowledge the whole team, "Dear Clarkesworld Team" works (listing all of our names is unwieldy).
Sometimes a writer doesn't know the editor's name. Sometimes it's difficult to find, or there's a whole list of editors on a website, but it doesn't say which one handles fiction. I get that. Just try really hard to get the information before sending in a cover letter that starts with "Dear Editors," which makes it absolutely clear to the reader that you don't know who's in charge. I admit that I've done it before when submitting stories, and now I have regrets. If you really don't know the right name to use, maybe try starting the letter with "Greetings" instead. But first, try again to learn the name of the fiction editor.
The last thing I'll get into today is the title of the story. The title is not just a label for tracking purposes. It's part of the story, a way to get the reader interested while emphasizing what is meaningful about what they're about to read. It should be neither a spoiler, nor something vague. I'm definitely not a title-writing expert just yet, but I know what I like. It should make me curious, and it should be relevant to the story, of course! I love quirky titles that twist my mind a little bit, so that I need to read the story to find out what's going on there. As far as I'm concerned, the title is just as important as the first sentence of the story.
Everything I've mentioned above has its place in the way that your submission is perceived. The story you send will have its merits and its flaws, no matter how you present it, but think of presentation as sending your story out for a job interview. Would you wear business clothes to an interview, or paint-spattered jeans and a ripped t-shirt? Given two candidates with equal quality but different presentation, which do you think would get the job?