Webgraphviz!

PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams. The generator can be run anywhere within JVM and integrated with various application such as wiki, text editor, IDE, programming language, documentation generator, and others. Mostly based on Graphviz. Can render various diagram syntax such as PlantUML, Dot, and Ditaa.

Graphviz is open source graph visualization software. It has several main graph layout programs. It also has web and interactive graphical interfaces, and auxiliary tools, libraries, and language bindings.

OmniGraffle can help you make eye-popping graphic documents—quickly—by providing powerful styling tools, keeping lines connected to shapes even when they’re moved, and magically organizing diagrams with just one click. Create flow charts, diagrams, UI and UX interactions, and more. Whether you need a quick sketch or an epic technical figure, OmniGraffle and OmniGraffle Pro keep it gorgeously understandable.

Gephi is an open-source software for visualizing and analyzing large networks graphs. Gephi uses a 3D render engine to display graphs in real-time and speed up the exploration. Use Gephi to explore, analyse, spatialise, filter, cluterize, manipulate and export all types of graphs.

Ever wanted to simplify documentation and avoid heavy tools like Visio when explaining your code? This is why mermaid was born, a simple markdown-like script language for generating flowcharts, Gantt charts and sequence diagrams from text via JavaScript.

Theory Maker is a free web app by Steve Powell for making any kind of causal diagram, i.e. a diagram which uses arrows to say what contributes to what. You make the diagrams just by typing the names of the elements (called variables) in a structured way into a (resizeable) window, and you get a live diagram as output which reflects what you type.