VivaGraphJS is the fastest graph drawing javascript library. It is designed to be extensible and to support different rendering engines and layout algorithms.
plotly.js is an open source, high-level, declarative JavaScript graphing / charting library.
plotly.js ships with 20 chart types, including 3D charts, statistical graphs, and SVG maps.
Cytoscape.js is a graph theory library for analysis and visualisation.
It's compatible with CommonJS/Node.js, AMD/Require.js, jQuery, npm, Bower, spm, jspm, Meteor/Atmosphere, and plain JS/JavaScript.