By graph here I mean something resembling these images:
When I did some work involving graphs last summer I found the best option that wasn't overly expensive was to manually do it in SVG, i.e. write out an SVG file from a bunch of strings, and render that out to an image using Inkscape.
This is not a quick and easy solution, but it does allow for near-infinite customisation, so it might be nice if you have to organise the graphs or do spatial organisation based on connections etc.