Tomasz Grajewski has posted this comprehensive tutorial on the Smashing Magazine site all about converting Flash games into HTML5 using Phaser: "The tips presented in this article aim to help HTML5 game developers in avoiding common mistakes when converting their Flash games to JavaScript, as well as making the whole development process run as smooth as possible. Basic knowledge of JavaScript, WebGL, and the Phaser framework is required."
The tutorial includes all kinds of useful tips, including how to replace the default Phaser shaders with your own, so you can support features like subtractive tinting or overdraw detection. Although based on Phaser 2, most of the advice given applies across the board and is well worth a read.