This is a bit off-topic, but I think there may be people here that has already dealt with this doubt.

When including a typical 2D plot, we usually put a label on the left border. My question is: do you usually add a symmetric padding, so that the figure appears actually centred in the text?

This is a document with two figures —the first one has been added a symmetric padding, while the second one has no padding at all:

MWE result

Which of both is the best option, according to classical laying-out rules?

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    Yes, I fear this is off-topic, since it has no TeX related content and is opinion-based too. Regarding the 'best padding', it depends on the style of document, on the margins (asymmetric margins -> asymmetric padding, to keep the illusion/impression of being centered`) – user31729 Jul 10 '14 at 8:29
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    If you're making a report on your research, you could try checking out some existing research journals to see what they do. In other cases it may not be that relevant how you do it, and in most cases I myself would end up using the "default" settings, because I often use multiple pictures in one float. When using multiple pictures the alignment won't visibly show because the caption will contain explanations based on Left: ... and Right: ... rather than just explaining the one picture in the float. (I hope it's clear what I mean.) – 1010011010 Jul 10 '14 at 8:51

This topic depends completely on your taste or on the question: "is the label part of the image or some side note". If you are asking for graphical design, you should refer to https://graphicdesign.stackexchange.com/questions/tagged/typography or alike.

As you have noticed that this topic worth to be discussed, you most probably do not like the "asymmetric" look of centred graphs. I personally do not like that as it interrupts all the nice centred, aligned, equally gray-coloured look, TeXing is giving me.

In order to give some on-topic advice here:

For the package pgfplots, which I recommend for nice graphs and plots in TeX, you may add the options trim axis left and trim axis right to your axis options. This will adapt the treated width of the graph to the length of your x-axis. More information can be found in chapter 4.20 of the pgfplots manual (7.6 MB).

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