MediaGoblin doesn't require JavaScript at all, much less proprietary JavaScript, and it supports any format. It doesn't need to not support bad formats to be good, though. RMS just has a desire to never have his talks distributed in those formats, ever, which I think is a little bit over-the-top, personally.

I'm not entirely sure, but I think MediaGoblin converts all files in a bad format to a good format on the server side, so that all media is available in a good format. At least, assuming the server has the software necessary to read the bad format. But that software is libre, so I would suppose that most of them do unless they have a particular reason to worry about the patents encumbering these formats.

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