The Isogenic Game Engine allows you to create games in both 2d and isometric and has built-in isometric depth-sorting, path-finding and even supports Box2d in isometric!
LimeJS is a HTML5 game framework for building fast, native-experience games for all modern touchscreens and desktop browsers.
Jaws is a 2D game lib powered by HTML5. It started out only doing canvas but is now also supporting ordinary DOM based sprites through the same API.
GameJs is a thin library on top of the HTML canvas element. In addition to the drawing functions it has a set of generally helpful modules for game development.