The elements of charting style

A graph that goes into a paper must never have a title (as in main=""). The title will be supplied by latex.
Both axes must always be annotated with units which make physical time sense. E.g. it's pointless to say "periods". Say "Months" or "Days". If you omit the units, it's almost always wrong. The only special case is time on the x axis, when I often omit the word "Time" since it's obvious by looking at the legend of the x axis.
Set the margins of the graph correctly so that you are not wasting whitespace.
Avoid using colour. Most people only have black & white printers.
Use good english as far as possible. E.g. never use a y axis legend like "lwpi". This means nothing to almost everybody.
Use an aspect ratio for the pdf which is sensible when it's put into a document. I.e. under normal circumstances it's got to be wide (e.g. 5-6 inches) and squat (e.g. 2-3 inches). Square graphs are a bad idea since they make no sense on all computer screens and page layouts.
When you have a legend inside the graph, it must be good English. Do not have strings like "Impulse.response" or "95%Lower.bound". COMPLETELY remove all notions of computerese when making a graph.
The font size of strings placed on the chart should be large enough so as to have adequate legibility.
Be careful about the aspect ratio. Sometimes, the insertion of a graph contaminates the aspect ratio and then it looks wrong in the end. Insertion of a graph into a document must never change the aspect ratio.