I think the best part of HTML5 Video is getting to convert the source file into a billion different formats for all the browsers (note: sarcasm). For a while I was struggling with Adobe's Media Encoder, trying to get that to do my work. It never really rose to the challenge.
Recently I've been using Adobe just for the FLV/FLA files (for flash fall-back) and then using Miro's video converter for the rest. It works a lot better, but is still not fool proof. I've found that the iPad and iPhone formats are still a little hit or miss when I test on the various iOS versions out there. What I like about Miro, though, is that I don't need to tune every parameter for the mp4. All I do is pick iPad and it takes care of the rest. Beautiful.
Another option is zencoder which has a nice API you can use. This would be a great option if you had to convert uploaded video or if you had a ton of video and you wanted to programmatically convert it. Just wanted to throw that out there.
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