Worked with Martin on the presentation of the 1907 Victoria video (an extension to this).

The player will load mp4 files directly, using a Flash Video (flv) as a fallback, but seems to choke on files as large as this (123MB). I have export the Victoria portion of the video to DV and will resize it to 480x360 next. Encoding will be H.264 (aka MPEG-4 AVC)

Of note here is the fact that Flash doesn't care what file extension you use for media. Videos need to be encoded using H.264. Audio tracks in videos need to be AAC, not MP3. Standalone audio streams can be MP3, however. A good post describing this in more detail is here. The author is an Adobe engineer working on the Flash player.