We host quite a few videos on our website, currently they are stored as flv files and played through a flash player (We user JW Player), but we get quite a few requests of people using non-flash devices (ipad, iphone etc) who want to watch the video and so I am quite keen to use the new HTML5
There are 3 main formats to consider: WebM, Mpeg4 and OGG. I used ffmpeg to convert the flv file to .mp4(codec h264) and .ogv (codec: ogg theora) files but found the quality better on mp4 and the file size smaller. I havent tried WebM so will leave that for a later experiment.
Best practice recommends that you should have available all 3 formats for each video with Flash player to fall back on (using the H264 video as Flash supports it). We have too many videos to have lots of formats supported, I wanted to keep it as simple as possible ie only have 1 format so I went with H264 mp4. The reason is: Flash supports H264 but doesn’t currently support Ogg files or VP8 codec. All the devices that cant play flash support H264.
Until I develop an automated system that allows me to upload a video and get it automatically exported into the different formats I will stick with mpeg4.