When designing your plots in gnuplot there is often a need to move labels and tics somewhere. In order to do so it is the best to make use of coordinate system explained here (to me, screen and graph are the most used).
Another annoying issue when designing plots to be inserted in the paper is the treatment of borders. It is especially distracting because of all scale-related issues (size, margin and so on). Some nice examples on the proper usage of different multiple layouts can be found here. And the nice overview of margin/eps/pdf cropping techniques can be found here, among which I personally prefer pdfcrop since I am using pdflatex.
In order to get the properties of the pdf file you can use pdfinfo or indentify. For instance, what I did to get the sizes of pdf pictures after cropping the border is
for f in *.pdf do pdfcrop --margins '10 0 10 0' "$f" "$f" pdfinfo "$f" | grep "Page size" identify -verbose "$f" | grep "Print size" done