Kinetic JS is “is an HTML5 Canvas library that extends the 2d context by adding region events for desktop and mobile applications, extends the 3d context by wrapping WebGL (…), and also provides animation support for both contexts.”
More info, and downloads: http://www.kineticjs.com/

EaselJS is a JavaScript library that “provides a retained graphics mode for canvas including a full, hierarchical display list, a core interaction model, and helper classes to make working with Canvas much easier.” Easel’s API “is loosely based on Flash’s display list, and should be easy to pick up for both JS and AS3 developers”.
Link: http://www.easeljs.com/

To make it even easier to convert projects from Flash to JS, the makers of Easel have released Zoe, “a tool for exporting swf animations as EaselJS sprite sheets”.
Link: http://easeljs.com/zoe.html

From http://mbostock.github.com/d3/:

D3.js is a small, free JavaScript library for manipulating documents based on data. D3 allows you to bind arbitrary data to a Document Object Model (DOM), and then apply data-driven transformations to the document. As a trivial example, you can use D3 to generate a basic HTML table from an array of numbers. Or, use the same data to create an interactive SVG bar chart with smooth transitions and interaction.

Via Miska Knapek.