Gnuplot in thesis and articles or not? I'm doing an astrophysics thesis with a lot of programming in Python. I'm currently using gnuplot for my plots, but I wonder if this is actually looking quite professional. Are there other options which look better and are still easy to use?

Here an example of a figure in my thesis:



The vertical line I got with the following command:   

set arrow from 4861.3,-1200 to 4861.3,2000 nohead lc 2  


I know it reaches out of the figure, but I use this command for all of my script and I know only at the end what the upper and lower boundary of the y-axis will be. Every peak is different.
If you do the programming in Python, you could also do the plotting in Python with matplotlib. With a little adjustment of the plotting parameters, it is possible to produce publication-quality plots with this software.

Alternatively, if you need fancy annotations etc., I can recommend the pgfplots package for tikz/LaTeX. You could export data from your Python program to a csv file, and then use that as data source for plotting with pgfplots. If you are also using TeX for the main text, it allows to to produce graphics which nicely fit the formating of the text.