When using gnuplot scripts to generate graphs in PDF format, there is the
size option. I would like to know how one can estimate the right size of the output graph to place in a scientific paper.
Output to a large size with a lot of whitespace (A4 is usually fine) and then trim the whitespace using
pdfcrop, a command line tool included in every latex distribution. See this great answer Pdfcrop is really reliable, so I do this for all my PDF graphics before I put them in my papers so tex can handle them consistently and I don't end up with weird tiny figures surrounded by whitespace.