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 had the same problem with IE9 showing a red cross when trying to show the .mp4 video. Keeping it simple using ffmpeg (as Michas suggested) solved the issue for me.
The ffmpeg parameters: (I used .ogv from ffmpeg2theora as my inputfile):
ffmpeg -i input_file.ogv -vcodec libx264 -vpre hq output_file.mp4
My ffmpeg version:
ffmpeg 0.8.3
libavutil 51. 9. 1 / 51. 9. 1
libavcodec 53. 7. 0 / 53. 7. 0
libavformat 53. 4. 0 / 53. 4. 0
libavdevice 53. 1. 1 / 53. 1. 1
libavfilter 2. 23. 0 / 2. 23. 0
libswscale 2. 0. 0 / 2. 0. 0
libpostproc 51. 2. 0 / 51. 2. 0