I've heard people say that plots produced by ORIGIN tend to look polished and "professional," whereas plots produced by Mathematica do not. However, most plot-creation programs are quite configurable and it stands to reason that with the right settings for things like tick location and labeling, font and color choices, label alignment, and so on, I should be able to make a figure with Mathematica/matplotlib/Gnuplot/etc. that looks as good as those that come from ORIGIN. But what does it mean for a figure to be "professional" in this context?
In other words, if my goal is to create the best looking figures possible for inclusion in a scientific paper, what design choices are generally recommended towards that goal? Obviously one has to choose the appropriate kind of plot, e.g. bar graph vs. scatter plot, and linear vs. logarithmic scale, but those are choices that we always think about regardless of which plotting program we are using. I'm more interested in the things we don't normally think about, which are normally set according to some plotting program's defaults, but which could be changed to improve the look of the plot.