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]



Before using yEd, I tried XMind and I like the colors and the look-and-feel. However, it cannot perform auto-arrange, and I have to manually reposition all floating topics. Floating topics are even harder to manage, since XMind is more for brainstorming where there is hierarchical organization of some topics. I can't even move the group of floating topics without disordering them. It looks like the one below.

[caption id="attachment_749" align="aligncenter" width="300" caption="Romans 8:28 using XMind"][/caption]

Personal Brain looks complicated to use, and it seems to behave like XMind, but I only spent few minutes trying the software. I was not able to run Prototype Composer because it requires .Net Framework 1.1 and I did not want to install .Net 1.1 just to run the program. I tried some web-based, and I'm also not satisfied with their features. Most of them are flash-based and they lack the ability to auto-arrange the nodes.

yEd works well and they have considered most of what I need especially in customizing the styles of the nodes and the edges. The default colors and styles of the edges and nodes are plain and simple. I customized them using the color and styles of XMind then I added these components to my palette so I can use them in creating new objects. The objects can even be grouped inside another box. Clicking the background creates new nodes, and performing a mouse drag gesture over a node creates an edge.

[caption id="attachment_750" align="aligncenter" width="300" caption="yEd Romans 8:28"][/caption]

I still need more time to study these representations I made. I'm not even 100% sure if using the available NLP resources, such representations can be made with high accuracy, and I'm also not sure if such representation correctly represents the meaning of the text.