For a good practical guide, I suggest reading this: http://www.amazon.com/H-264-MPEG-4-Video-Compression-Generat...
It'll give you an idea of where all the settings come from.
The Doom9 stuff seems to be more oriented toward ripping and encoding for personal use, not taking a source file and encoding several versions for streaming from a Wowza Media Server, Red5 server, or Flash Media Server...unless I am not looking in the appropriate place.
I haven't yet looked through the flowplayer forums. That seems like a good idea.
That book you linked to has a newer version, but it is over $100.
IF not CLI examples, would you have any recommended settings for encoding to stream for multiple devices and connection speeds (iDevices, Android phones, flash video)? What bitrates and resolutions from a 1280x720 60fps source file?
I think you will find preset in the ffmpeg source/ffpresets
Very important : once you get ffmpeg to work just the way you want, back up the source that you used to build your binary and backup all sources of libs . This is important as sometimes refreshing code from repositories breaks the features you depend on . And if you are extremely paranoid like me and your business had a critical dependency on video transcoding, create a Virtual box guest OS, build ffmpeg and tweek till it works and then save that image for emergencies. Its about a Days work in all.
I have a shell script that scans my "input folder"(an ftp dir) once it finds a file , it invokes ffmpeg process. On a quad core box, I max my cpu utilization at 8 ~10 concurrent instances of ffmpeg. Your mileage would depend on factors like bitrate etc.
By the way, this will give crappy audio quality due to ffmpeg's garbage aac encoder. What I did was shut off audio in ffmpeg (-an) then I used Nero AAC encoder to encode the audio. Then mp4box stitched them together.