Paper.js - Open source vector graphics scripting framework that runs on top of the HTML5 Canvas.
GoJS - GoJS is a JavaScript library for building interactive diagrams on HTML web pages. Build apps with flowcharts, org charts, BPMN, UML, modeling, and other visual graph types.
p5.js - JS library for creating graphic and interactive experiences
mxGraph - mxGraph is a fully client side JavaScript diagramming library - jgraph/mxgraph
Three.js - A JavaScript 3D library which makes WebGL simpler.
JointJS - Create interactive diagrams in JavaScript easily.