"As a software developer, I used to use Graphviz for my code comprehension needs. While its compact format has its advantages, it was just too much effort to input data - particularly relationships. I wanted to be able to create relationships by dragging my mouse from one node to another. This is exactly how yEd works.
You don't have to sacrifice the longevity of plain-text that Graphviz files offer. yEd works entirely on the XML-based GraphML format. You get the same benefits of cross-platform support and exporting to SVG, PNG, PDF etc. as with Graphviz. But yEd is that it is written in Java yet has a 100% native look and feel (so on Mac, you can zoom in and out with 2 finger scrolling).
The best feature for me is its ability to group nodes and collapse/expand them. This makes it possible to capture much bigger graphs in a single file than with Graphviz (in which I had to mess with numerical properties). Layouts also give you the ability to comprehend your data in different ways, and when you change layout it animates the transition which makes the experience fun.
yEd, which is free, is probably better than any non-free software out there, and I've never had to upgrade it since I first heard of it, and haven't noticed any bugs. I'm really grateful for yWorks for this product and hope it stays around as long as I live."
Sridhar Sarnobat (Software Engineer at E-Touch Systems in Fremont, CA)