It depends on the level of detail you want, but any graphics package could allow you to do something like the Underground map - after all, part of Harry Beck's genius was in realising that when it came to the Underground, physical geography was less important than links - where you're connected to is far more important than where you are.

Other than that, I'd suggest trawling the Traveller RPG websites - there's an awful lot of software written by fans for that.

You might also want to look at the Fading Suns websites, because as far as I recall, they use a very similar system of stable jump gates linking solar systems.