The nice thing about Ggnuplot is that it's extremely easy to connect it with anything, since it's basically its own language. Python has made a lot of inroads into the scientifc computing field but it's by no means the only one. This is a field where twenty year-old Fortran libraries are still relevant.

SVN also has the important advantage of being relatively easy to pick up by someone who's not a programmer. It would not be my first choice for a version control system now that we have Mercurial and git (frankly, it wasn't not even back when our only affordable alternatives were CVS and RCS), but it's very easy to teach it.