I use a MS Word I've tweaked to turn off autocorrect, grammer check, automatic tabbing at the start of a paragraph, and tweaked to put some extra buttons on the top bar such as "word count" and "thesaurus". I've also changed the normal.dot template so it defaults to 12 pt Arial font (although sometimes I mistakenly hit some weird key combo and it goes back to Times New Roman), and I type single spaced. I also do a centered * * * * betwen scenes rather then a centered # - this dates from the days when I wrote longhand in a notebook, I used to put four stars between scenes.
Really, the only thought I give to the final formatting is making sure my italics are underlined, just because I'm not aware of a way in Word to make italic words underlined all in one go, and it would suck to eyeball it line by line when formatting it, trying to spot all the italics and make them underlined.
Edit: Regarding habits, just in case some folks don't know yet...I use these shortcuts while typing:
shift + arrow keys => highlight a word so I can type over it, or underline it, or manipulate it
ctrl + I => italics
ctrl + B => bold
ctrl + U => underline
ctrl + home key => move cursor to the very start of the document
ctrl + end key => move cursor to the very end of the document
home key => move cursor to the start of the line
end key => move cursor to the end of the line
ctrl + c => copy highlighted text
ctrl + x => cut highlighted text
ctrl + v => paste text where the cursor currently is.
ctrl + s => save document