[lupire]

Pro tools like Omnigraffle handle that sort of thing. Best of both worlds.

[riffraff]

And omnigraffle can take a dot definition as input and the let you fiddle with it manually, it is really a joy to work with.

[hatmatrix]

yEd is freeware (not free software) but I have not found a better program that matches accessibility (Java-based so runs cross-platform) and sophistication in automated graph layouts.