Best and Free Diagram and Graph Maker

I've been finding a good, free, and easy to use diagram or graph making software. I'm doing some experiments on visualizing some natural language representation. I need to do this manually so I can easily study and compare different representations. I need a tool that can allow me to easily add nodes and edges, and customize the colors. The program must be able to arrange or to layout the nodes and the edges. I was able to try yEd Graph Editor, a free Java program, that allows me to create something like the one below.

[caption id="attachment_748" align="aligncenter" width="300" caption="John 3:6 using YEd Graph Editor"][/caption]