I am using FFMPEG to convert a video to .mp4, ,ogg, .webm so that it may be viewed in all HTML5 capable browsers using the video tag
I tried a lot of video files, encoding options, server configurations, FFMPEG versions, other video encoders etc. before finding out that one thing to consider when serving MP4 files for IE9 is the file meta information called moov atom embedded in the MP4 file itself. If it's located at the end of the file, where some encoders including ffmpeg places it, IE9 will not start playing the video unless the whole video file downloaded. Relocating the moov atom metadata to the beginning of the file enables progressive download of the MP4 file, and IE9 handles the video nicely.
There's a tool called qt-faststart to perform this operation. Worked wonders for me, compiling and using the Linux command-line version distributed with ffmpeg.
make tools/qt-faststart
sudo cp tools/qt-faststart /usr/local/bin/
qt-faststart original_file.mp4 modified_file.mp4