What exactly do you want to do? Feed data files and have the graphs visuaized, or draw and edit them by hand?

Like I mentioned in a previous post, I use Pajek. It seems like it can do a lot, and is free.

Anthony,
here's the list of graphing programs:
www.insna.org/INSNA/soft_inf.html

I've tried netdraw, which is free and works ok. I've also tried pajek which seems to offer more features, but I don't think it offers the command-line interface I need to interface with php.

Most of these programs are research projects, have very poor usability and many are still having features added. I also get the impression that they have been built from a technical perspective (do we have the latest layout algorithm installed?) instead of a task-oriented rationale (have we supported what people are trying to use it for?).

I suggest using something like php to read in a data file in your own format (e.g. excel) and translate it into the syntax needed for the file format by your program. Getting data into them is a real pain.

You might also try the web based www.netvis.org
best of luck.

Since I have no idea how much data you need to work with, I'll tell you about what I use: yEd. Its probably only good for smaller #s of data points so that you can input it by hand individually (rather than plug in a huge textfile full of data) but its very user friendly. Actually, a little frustrating at first but only 1/10 of the effort it takes to understand GraphViz (which I've given up on already.) (it was only frustrating because it was the first time I've worked on any data vis. program)

www.yworks.com/products/yed/