I use the annotations feature of YouTube a lot, but I want to get away from flash and start hosting my videos using html5. So I need to create those bubbles and embed them in the video using an editor. Is there an easy way to do that or a video editor that has such feature?
Not directly answering your question, I would say hard-embedding them on top of your video is way too destructive. YouTube agrees with me; they don't edit the videos you annotate, they just show a deebrie above the video.
And you can do exactly what YouTube does with your HTML video. The difference is you need to do it. In short: load a list of annotations (their text, time, duration and position), listen to the playing event of the video, and the pop up divs over the video while it's playing.
There are HTML5 "players" out there (they're more frameworks around the