Here is the criteria for a "perfect" graph editor:


* it should be able to perform an automated, but controllable layout
* one is able to make "manual" enforcements to nodes and edges locations when you need it (or at least such fine automated layout so you don't need "manual" enforcements)
* one could add some math symbols and formulae on a graph


Common vector graphics editors could do the trick, but there is a lot of overhead efforts to draw every node, every edge, every label.


Graphviz is good enough, but sometimes you cannot get needed layout (even if you use several tricks like additional invisible nodes etc) and you should use ladot or dot2tex for math formulae


yEd has nice layouts, but there is a problem with a math text.


This is probably not a math question, but it is common to draw graphs in articles i think.


[Result graph](http://mathtech.ru/0pocket/grf_res.jpg)


(Update: 27.12.2010)
Here is another candidate for the best editor in TeX - Asymptote (asymptote.sf.net).
The very powerful tool at first glance.


(Update: 28.04.2014)
The very tasty semiautomated tool to use with PGF/TiKZ is TiKZEdt. You can extend its palette with your own tools and make the process of diagram creation very simple!



What is the best graph editor to use in your articles?
I already had about 30 pages of graphs typeset with xymatrix for my thesis before discovering tikz; but was so impressed by it that I was happy to rewrite them all. As well as (imho) looking better, it gave me cross-platform compatibility - xypic seems to need pstricks, so on the mac with TeXshop (which uses pdflatex, I assume) the old graphs couldn't even be rendered. 


Its ability to construct graphs iteratively can also be a massive timesaver- for instance, I wanted a bunch of otherwise identical rectangles at various positions, so with tikz could just loop over a list of their first coordinate rather than having to tediously cut,paste and modify an appropriate number of copies of the command for a rectangle. Particularly handy when I then decided they all needed to be slightly wider!


There's a gallery of tikz examples [here](http://www.texample.net/tikz/examples/), to give you some idea of what it's capable of (and with the relevant source code- I did find the manual a bit hard to understand and learnt mostly by examples or trial and error).


The vector graphics package inkscape (which I used to use for drawing more complicated graphs for inclusion as eps images) also apparently has a plugin to export as tikz, although I haven't tried that out.


