Figures are not an afterthought
Your figures will form an integral part of your publication - people often read an abstract and then look at figures to get an idea of the main points of the paper, and to decide if the paper is worth reading further. Therefore your figures need to be carefully chosen to make sure that they tell as much of your story for you as possible. Plan out your figures as part of the process of drafting an outline for your manuscript so that your figures and text complement each other without repeating information. Selecting effective figures can help to engage reader interest and increase comprehension (and therefore hopefully your citations!). It can also help to decrease word counts, as lengthy text explanations can be replaced with succinct figures. What makes a figure effective will vary between fields and disciplines, but overviews, trends, and spatial data are all good candidates for information that might be better displayed in a figure rather than described in the text.
As you plan your manuscript, you should have some idea of the publication you intend to submit to. The author guidelines on a publication's website will often contain information on requirements for figures, such as the number of figures allowed, minimum font size, required file formats and resolution, or the column width that the figure will need to fit into. Guidelines vary between publishers, so always make sure you know your publisher's requirements, and follow them throughout the process of creating your figures. Plan for your figures to fit either a single column width or across the full page, and then make sure to create them at that size. A common mistake is to draft figures very large, and then shrink them down to fit the allotted space. This frequently results in features of your visualisation becoming minuscule and illegible at the new size, requiring you to redraw your figure and re-size all annotations.
Figures should "stand-alone"
All of the information necessary to understand your figure should be contained within it. Figures may end up being reproduced or presented separately from manuscript text, for instance if they are used in a presentation, in which case any explanation or context provided by the text would be lost. To make a figure self-contained ensure that:
Consider your colour
Even though many journals can be accessed online and people tend to obtain electronic copies of articles, figures in papers stand a high likelihood of being reproduced in black and white at some point. This may be because the print version of a journal is only black and white, or charges extra for colour images, or could occur when readers print a hard copy of a paper. If colour was used to convey information in these cases, the resulting black and white figure could become useless. It's a good idea either to create greyscale versions of your figures for the print versions of journals, or, even better, to choose a colour palette that can be printed in black and white such that the colours are reproduced as distinguishable shades of grey. ColorBrewer is a good resource to help you create suitable colour palettes. Doing this will also help to ensure that your figures are accessible to people with vision impairments, such as colour blindness.