Permission

Submission of a paper requires permission from a senior member of the group. Your institute might have more formal procedures. The reason behind this bureaucracy is that the content and quality of the paper reflects back on the whole group, and on the whole institute. This connection has moral and legal sides. Not following these procedures can have very serious consequences. If you want to send in a paper at your own responsibility only, use your private home address as affiliation and refrain from using any facilities of your employer.

Submission letter

Reasons for publication should be in the paper. You could describe in four or five lines the important conclusions of your work for non-specialists. Many journals request this popularized summary explicitly.

Add a sentence that these referees have not been contacted by any of the authors, and have not been informed in any other way about the content of this paper.

Asking the editor to exclude a referee, who you know is hostile towards your work or person, is dangerous. The editor might be tempted to use him out of all people. If you want to rule out a hostile referee, explain to the editor why you want to bar him.

Few people can resist the temptation of a boosted citation record.

Nature and Science

A number of prestigious journals, like Nature and Science subject the manuscript to a real test before they send it out to referees. I hate this but I am not a Don Quixote. So I also submit manuscripts to them.

You can influence this process in a number of ways. Firstly in the manuscript itself. But also in the correspondence accompanying the submission process.

Manuscript