Also no graphviz![0] I know gephi is gaining a lot of ground, but for a wide range of visualizations requiring actual graphs it is still very hard to beat the simplicity and power of graphviz.
It's a pity that gephi is loosing the edge recently. The development is quite stalled and few things have changed since 2 years ago. It's even pain to get it to work on mac as it works only with java 6 and will not work out of the box :(
...and no mathplotlib, either... I even don't like python that much, but you have to recognize mathplotlib... but hey, at least they got pizzapiechart.js...