Zombie nouns and aggressive passives: kill that "office-speak"
The only "rules" of writing are your rules. But you need to decide what they are.

You will never annoy anyone if you present a manuscript like this

Well, I can't absolutely promise that, but pretty darned close. Of course this is subject to whatever the magazine, publisher, agency or editor says on their website that they want. And we are talking prose, here, not scripts or poetry, which run by different rules. But don't think that, just because we're in the digital age, what's used on computers has superseded what's used on manuscripts. The book is near-perfectly evolved technology for reading large amounts of prose, and the book and magazine trade still handles prose in those paper-based forms, even on screen. Digital design has evolved to suit a completely different technology.

Yes, I know it's boring; I too love typography and fine printing, and sympathise with Jonathan Falla when he says that getting the visual form of his words wrong on the page would be like "serv[ing] whisky in a styrofoam cup". Yes, I know that to make your life simple you might have to tinker with the settings in Word so that more of what's needed happens automatically. Yes, you will hear stories of a writer who hand-wrote his entire 190,000 word epic in the blood of freshly-slaughtered virgin sheep, and got a book deal but, believe me, that's the exception. (Not least because the advance didn't pay enough to cover the bribe to the slaughterman.)

The point is that when you're offering work to agents and publishers, you have to stop thinking like a writer, with all the stubborn creativity, necessary individuality and cat-like reluctance to be herded that we have, and instead imagine yourself into a weary slushpile-reader's brain. Formatting your work this way makes it as easy as possible for your actual words and stories to slip into the editor's mind and lodge there.

And if you're sending work to someone for an appraisal, do you not want to have the same effect? I know one vastly successful and experienced editor/teacher who states on her website that she'll charge twice her normal rate if the MS doesn't arrive in industry standard format, because (a) it makes it so much harder and slower to read, and (b) she feels that anyone who's taking their writing seriously enough to want her help should take presenting it equally seriously.

That means conforming to what the book trade knows makes manuscripts as easy as possible to read. Agents and editors are kindly souls and also hate the thought of missing a diamond by being too prescriptive, so they may say they'll read anything sensibly presented. But some sensiblies are much more sensible than others. And it also means engaging your bog-standard common sense about the realities of office life and busy professionals, which seems to desert many writers when it comes to these issues. (For example, you wouldn't believe how many manuscripts I see which don't even have page numbers.)

Perhaps it's worth also saying that your industry readers are not expecting something that looks like a book, with all the detail of design and typography that the designer and typesetter will go into. You might like to do it for yourself, as a way of helping you to read your own work as a reader would; but don't send work out in that form. The book trade got on perfectly well in those not-so-long-ago days when "manuscripts" were typescripts: actually typewritten. True, putting something in actual italics has superseded the underlining of it, which was the typesetters' code for "italicise this". But other than that, you really don't have to worry about doing the things that a typesetter will do, like setting out block quotes. A manuscript is a tool for producing a real book, not the first shot at that real book. Clear and sensible is what matters.

So here is a basic, sensible guide to producing that clear, sharp tool:

  • a .doc or .docx file. So: not .rtf, not.odt, not .txt, not whatever it is that your iPad does; and, above all, not the wholly infuriating .pdf, which produces monster files and needs expensive programs or flakey free ones before it can be worked on. A Word document is still the only format you can rely on everyone being able to cope with without faff, and if yours needs faffing with they just might not bother.
  • at least 2.5cm or 1" margins all round. Because (a) the human eye can't track a line longer than about ten words, without becoming unreliable in getting back to the start of the next line. And (b) we all still do scribble in margins.
  • double-spaced lines. Again, to do with (a) how the human eye tracks a line, and doesn't want to get muddled with the next line, and (b) how the human editor marks up. One-and-a-half spaced if you absolutely must, but try it with your font and point-size to check it's still easy to read.
  • no extra space between paragraphs. Keep that for when you want to indicate a section break or a jump in time or place; otherwise it feels, to me at least, as if the story's stop-starting like the engine of a hybrid bus. Also saves vast amounts of paper.
  • indented first line of the paragraph by about 1.25cm/¾", because of the no-extra-space. The paragraph is the basic unit of your storytelling, so we must, without having to think about it, experience the new-startingness of this new paragraph. Three-quarters or even a whole inch is enough to make the new start clear, not so much the eye has too far to go to get there.
  • text "ranged left" not justified. i.e. with an even left-hand margin and a "ragged" (not even) right-hand margin. Justification as done by a computer, rather than a skilled typesetter, often results in a mess of some lines having about three words in them, and others so squashed up it looks awful.
  • 12 point size Not smaller. Most agents' and editors' eyes are very, very tired. Probably not bigger as it can look a bit primary-school.
  • a serifed typeface/font. Serifs - as in Typepad's versions of Times New Roman or Book Antiqua- evolved to lead the eye along a word, a line, a page as swiftly and steadily as possible. You don't know better than 1,000 years of literacy, nor than geniuses like Christophe Plantin and John Baskerville, so don't try to use a san-serif face like Helvetica or this blog's Georgia.
  • ideally Times New Roman. Yes, it's boring, yes it's not very beautiful. But it's the industry standard. It also gets the maximum number of words onto a page, which saves everyone's paper.
  • consecutive page numbers in the header. This is not optional, but easy to forget if you don't routinely work in "page view". Don't forget.
  • title page with title, your name, your address, email and phone number.
  • good, black print if you're printing out. This is not the moment to set it to 120 dpi, nor to scrape the last drops of ink out of a fading cartridge.
  • if you're sending hard copy, no staples, no paper-clips, no binders of any kind: they all cause problems. No need to put a thick ms in a folder: a couple of elastic bands will keep it together. Put the whole lot in a sturdy envelope. Don't forget a full-size stamped, self-addressed envelope if you want the script back; a note and a small stamped s.a.e. for the answer if you don't.

And here are some optional things to consider

  • make the filename something helpful. Means they're never puzzled by a mystery file, or can't find yours. "BTSA" or "YSBT", let alone "Final Draft", may say a lot to you, but nothing to Star Agent. How about "YourSurnameBookTitle" or "BookTitleStarAgent"?
  • put an indication of the date in the filename. TitleNameNov15, say. If you send it to anyone, if/when they send it back, you'll be able to see its relationship to what you're working on now. 
  • "YOURSURNAME/BookTitle" in the header (or footer). Or the filename if that's something explanatory. Or both, one in the header, one in the footer
  • date of printing/sending in the footer. Does no harm to have logged when they would have got it. And it's handy when you get it back, if you've acquired new versions in the meantime. 
  • page numbers in the footer as well the header. Personally I prefer the look of an empty header-margin, and put the page number in the footer. But the day my agent said "For example on page..." and I saw her eye flick up to the top, and only then find the bottom where the number actually was, I saw the error of my ways, and added it to the top, to accommodate different defaults.
  • more like 1½" or 3cm margins at right and left. The slightly more spacious page looks good, and gives us more space to write on
  • paragraph indents done with Styles. Not the tab, which may well get chewed up, especially by an e-reader. And please, please don't do indents with the spacebar.
  • for entering a competition, make a new file and take all identifying names and email addressed etc. out. Assuming it's judged anonymously, obviously. If you want to tweak a file to send to a new agent or publisher, personally I would also make a new file for that tweaked version: it's horribly easy to forget that they've asked for the covering letter to be in the same file, and three months later send the whole thing to Agent Two, complete with letter to Agent One. 
  • get a small laser printer. You won't believe the speed, print-quality even at low resolutions, and miniscule per-page cost, compared to your inkjet. 

And, to be brutal, if you still feel that presenting your precious work in industry-standard plain-vanilla will be a betrayal of your innermost creative being, which can only be truly expressed in the typographical equivalent of salted pistachio caramel with estate-grown chocolate sauce, then either (a) be resigned to not getting very far in the industry, or (b) get over yourself.