Many tools are available to make and edit HTML5 video and caption/subtitles:
Tools for converting existing file formats to WebVTT files, such as Simple SubRip to WebVTT converter, which is popular in the DivX/AVI/Mkv/mp4 scene. Do a quick Web search and you will get plenty of other results.
Tools for creating subtitles/captions from scratch. Use these to generate a WebVTT file. You can embed the <track> element in your own videos, on your own Web pages, or upload the WebVTT file to YouTube. We recommend amara. It's a free online tool that is very easy to use. There are also apps such as Subs Factory (Mac OS), Subtitle Edit (Windows), and Gnome Subtitles (Linux).
Enhanced HTML5 video players that use the <video>, <source> and <track> elements under the hood. They also provide many extra features, including support for subtitle/caption formats other than WebVTT (by converting on the fly).
We do not claim that these are the best tools, so feel free to share your discoveries in the discussion forum!