The goal of a manuscript is to be read–so it should be readable. Everything else is secondary. A few things make documents readable:
1) A 12-point serif font. There are many that are OK. The Times family is fine, or Garamond, or Minion. Courier is OK–but why? It looks like a typewriter and makes poor italics.
3) Consistency with special characters (em-dashes, ellipses, etc). We don’t care if they’re not exactly the way they will be typeset–search and replace is easy. But if they’re consistent, it’s only necessary to search and replace once. It is rare to have cross-platform issues nowadays, so it doesn’t matter if you have a Mac or a PC or older or newer versions of word processing software. If you use Greek letters, use the Symbol font.
4) Word count. The computer word count.
There are quite a few odd pieces of advice you will see out there, most of them holdovers from the days of lead type and/or clunky software. Some publishers demand Courier and/or a word count based upon Courier; some reject a manuscript over trivial formatting issues, such as two spaces after a period. Honestly, we do not care. Everything will be re-formatted for both e-publication and print publication anyway. All that matters for us is content and readability.
(And a ducky somewhere, of course. Quack!)