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Then based on that, you really only need two video formats: H.264 in some universal container (i.e. mp4, or m4v, whatever you want to call it) and WMV. The H.264 content goes in the mp4 file. It will be playable in Flash*, Quicktime, VLC, and under HTML5 in iPad, Safari, and Chrome.
The WMVs are still a good choice, especially for downloadable content. You might consider offering a Silverlight player option for the WMVs, instead of, or in addition to, allowing downloading. There are a number of open source Silverlight players that are pretty good.
*Bear in mind that H.264 support is limited to Adobe Flash Player 9 version 3 and later. Most people have this, but for those with an earlier version they'll need to upgrade. Flowplayer itself requires Flash 9 or above, and you can include an extra check in the Flowplayer code for update 3 like this:
$f("player", {src: 'flowplayer.swf', version: [9, 115]}, {
// configuration
});
More on the Flowplayer site. If users have an earlier version, you can either require them to go with WMV, or fall back to a third version of the videos in FLV/VP6 format. This is how YouTube does it.
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