The margins should be one inch all around so the editor can make notes (less important, but still standard, for electronic subs).
The author's contact information, including (real) name, mailing address, telephone number, and e-mail address goes in the upper left-hand corner and is single-spaced.
Halfway down the page, place the center-aligned title. One double-spaced line below that, write "by" and the author's real name or pen name, if applicable. Double-space again and list the manuscript's word count. I like to use "'x number' words" notation. Don't worry about the arcane methods editors once used for tallying up the number of characters in a manuscript. Just use your word processor's word count.
Now that you're on the actual first page, create a header to be displayed in the upper right. This header should appear on every subsequent page of the manuscript and should at least include the author's last name and the current page number, separated by a forward slash. The title (if it is short), or a significant element from the title, can also be placed between the author's name and the page number, also separated by slashes, e.g.: Farmer/Big Heist/1
For short stories, reproduce your contact information on the first page of the manuscript in the same format and position as it appears on the cover page.
Place the word count in the upper right-hand corner of the first page (not in the header).
Proceed halfway down the first page and write the story's title again. Double-space down and write "by" and the author's real/pen name.
Double space down twice, indent, and begin composing the story. Make sure the body of the text is double-spaced.
I used to agonize over the proper choice of font. Courier 10 pitch used to be the standard for everything from novel manuscripts to screenplays, but some editors hate it. Honestly, your best bet is Times New Roman, but you can get away with anything except Comic Sans. Your entire manuscript, including all of the information on the cover page, should appear in the chosen font.
An optional touch that editors love is if you create customs styles to handle all of the font/spacing/indentation formatting in your manuscript. You can find a handy guide to making your own custom MS Word fonts here.
That's about it. You shouldn't write "The End" at the end of a manuscript. It's OK to just write End. In fact, it's probably best not to write anything after the last word and punctuation mark of the story--especially if you're trying to squeeze in under a word count limit.
Note: above all else, always make sure to read, understand, and follow the submission guidelines of the market you're submitting to. Flagrant violations of a magazine's--or worse, a contest's--submission rules is the best way to get your work filed directly in the trash.