Make your points.
Decide what are the key conclusions of your work and state them clearly and succinctly in the Abstract and in the Discussion and/or Conclusions sections. Far too many papers say that “important insights were gained”, but do not explicitly state the insights. This leaves the reader suspicious that no insights were, in fact, gained.
Be mindful of the context of your work.
A research project takes place within a specific intellectual and social setting, and a sophisticated paper is written with this context in mind. The consequences include exploration, brief or lyrical, of potential implications of your results; acknowledgement, muted or forceful, of related controversies; and well-chosen terminology.
Beware of writing long, boring descriptions of your results. Focus on the results that support your conclusions. The other details can be summarized in tables, figures, and/or supplementary materials. Paragraphs should almost always be less than 1 double-spaced page in length.
Scientific papers are intrinsically hard to understand; consistency can make yours easier to read. For example: Use consistent terminology even at the risk of seeming repetitive. Clarity is more important than elegance. (Thanks to Barry Honig for this paraphrased advice.) The order of the rows of data tables should match the order of presentation in Results. Then your reader can follow the text by going down the rows one by one. The column headers of your tables should be consistent across tables. For example, if you use G for free energy in one table, use it in the other tables as well.
Use correct grammar.
Incorrect grammar is jarring to the reader; more importantly, it obscures your meaning. Do not expect your reader to finish reading a paper whose every sentence must be deciphered. If English is not your native language, don’t hesitate to get help! Many universities employ professional grant writers who can also help with your papers.
Be sparing with italics and bold font
Use italics or bold font only when powerful emphasis is needed. Overusing these font changes will make your text cluttered and sloppy and will also deprive them of their ability to focus the reader’s attention. Avoid the temptation to use italic or bold fonts to rescue unclear writing. It doesn’t work. Italics and bold font read as a raising of the voice and are similarly ineffective at generating clarity.
Make your figures clear and simple.
A figure is a way to help your reader to understand your data more easily, so strive for clarity and simplicity. Give the most significant or authoritative curve in a graph the most authorititive appearance; typically, this will be a heavy, dark-colored, solid line. The other lines can be made dotted, dashed, lighter in color, etc. The most significant or authoritative data might be from the most reliable experiments or the highest-quality calculations, or from a novel method with which other methods are being compared.
Unless you are skilled at embedding tables and figures in just the right places in the text, put them at the end of the paper, subsequent to the citations: tables first, and then figures. This will allow your reader to find them easily. For in-house drafts, it is helpful to place the table captions and figure legends directly below their respective tables and figures. However, you may need to group the legends in a separate section in the version that is submitted for publication.
Color figures are appealing but may be costly to print and they do not add genuine value to a figure if it can be rendered equally clearly with black and white. For example, three curves in a graph can be readily distinguished by making one solid, one dotted, and the third dashed. When you do use color, avoid gaudiness. The default colors provided by Excel are neither visually appealing nor particularly clear, so do not rely on them for presentation-quality graphics.
Cite prior work
For the sake of documentation, not to mention courtesy to your colleagues, almost every statement of scientific fact – or supposed fact – in a paper should be accompanied by a citation. Exceptions are typically made for time-honored textbook material, such as Coulomb’s law, or possibly other information that may be regarded as generally known; but when in doubt, cite.
Provide supplementary materials.
A paper is supposed to allow the reader to reproduce your work. This ideal is not always achievable, but providing supplementary files of data, structural information, methods, graphs, etc., can go a long way. It is also an act of good scientific citizenship.
Put the date below the title and author list each draft of a work, so that a reader with two versions of it can be sure of reviewing the latest one. Include page numbers so colleagues and referees can easily reference sections of section when discussing the paper with you. Make sure Figure and Table number matches the text correctly, even in a rough draft, so that your colleagues do not waste time struggling to determine which figure or table you are describing in the text.
Use fonts and line spacing that are easy on the eyes. These are simple things that take only a few extra minutes when preparing your manuscript, but they can make a big difference to the experience of reading it. Remember: the idea is to make the editor’s (and reviewers’) life easier, not harder.