What bunch of ffmpeg scripts do I need to get HTML5-compatible "Video for everybody"?
Note: This answer was heavily edited since its original posting. It's 2017 now; streaming works differently than it used to. This guide assumes simple progressive download of one video stream at one given resolution – no adaptive streaming.
Requirements
First off, make sure to download a recent ffmpeg version (download a static build; don't call apt-get install ffmpeg or similar). Ideally, compile it yourself. It doesn't take too long.
To generate videos supported by the most browsers, always check the latest compatibility table. There is no single codec/format that works in every browser, but if you generate H.264 in MP4 and VP9 in WebM, with the respective audio codec, you will have support for Chrome, Firefox, Safari, and some versions of IE.
WebM (VP9 / Vorbis)
Follow the recommendations in the FFmpeg VP9 guide and use a two-pass encoding approach with rate constraints:
ffmpeg -y -i input-c:v libvpx-vp9 -b:v 2000k -minrate 500k -maxrate 2500k -c:a libvorbis -pass 1 -f webm /dev/null && \
ffmpeg -i input-c:v libvpx-vp9 -b:v 2000k -minrate 500k -maxrate 2500k -c:a libvorbis -pass 2 output.webm
The target bitrate depends on your resolution, frame rate, the type of content, and what quality you want. 2.5 MBit/s should be a good compromise for HD video at 30 fps. See this Google guide for some recommendations.
MP4 (H.264 / AAC)
Follow the recommendations in the FFmpeg H.264 guide and use a two-pass encoding approach with rate constraints:
ffmpeg -y -i input -c:v libx264 -b:v 5000k -minrate 1000k -maxrate 8000k -pass 1 -c:a aac -f mp4 /dev/null && \
ffmpeg -i input -c:v libx264 -b:v 5000k -minrate 1000k -maxrate 8000k -pass 2 -c:a aac -movflags faststart output.mp4
Here, the target bitrate should be about 50% higher than for VP9 video, as H.264 is not that efficient. Add the -movflags faststart option to the second pass to make initial loading of the video faster.
For setting audio options, see the AAC encoding guide.