I'm at a similar stage, and I have settled on Transloadit (http://www.transloadit.com http://www.transloadit.com) for encoding and storing on S3, and the HTML5

I'm at a similar stage, and I have settled on Transloadit (http://www.transloadit.com http://www.transloadit.com) for encoding and storing on S3, and the HTML5 VideoJS player (http://www.videojs.com http://www.videojs.com) - which falls back on FlowPlayer for Flash, for playing the output video on the website. My experience with all three of them has been fairly positive, if not excellent.