Litegl.js
Lightweight Javascript WebGL library for handling Context, Meshes, Textures and Shaders. Relies on glMatrix 2.0, very easy to use.
X3dom
X3DOM. A framework for integrating and manipulating X3D scenes as HTML5/DOM elements.
Shader School
A workshopper for GLSL shaders and graphics programming
GLSL.js
A light Javascript & GLSL library for vizualisation and game purposes (2D or 3D).
Philogl
A WebGL Framework for Data Visualization, Creative Coding and Game Development
Glow
GLOW is a WebGL wrapper, which focuses on easy creation and use of shaders.
Gl Boost
A Useful WebGL Library for Small Turning
Ejecta
A Fast, Open Source JavaScript, Canvas & Audio Implementation for iOS
Scenejs
An extensible WebGL-based engine for high-detail 3D visualisation
Sylvester
Vector, matrix and geometry math JavaScript
Cannon.js
A lightweight 3D physics engine written in JavaScript.
Glslify
A node.js-style module system for GLSL!
Whitestorm.js
WhitestormJS physics + rendering of 3D
Css Camera
New way to see a web page with CSS3 3D transform
Oimo.js
Lightweight 3d physics engine for javascript
3 Dmol.js
WebGL accelerated JavaScript molecular graphics library
Three.js
JavaScript 3D library.