configure ffmpeg to create mp4 videos for flash, html5 and mobile phones

With have a Linux server with AMD64, Debian and ffmpeg 0.6.1 installed. When users upload videos we need to convert them to a standard format. In the past we used .flv for our flash frontend. Now we want to produce .mp4 files that can be played by flash (h264 and aac), are html5 compatible. We have installed, configured ffmpeg ourselves so that libx264 is enabled. We have so far not managed to produce proper mp4s. The task is to make it work: 1. provide a ffmpeg statement that turns input video files into proper .mp4 files 2. adapt our [login to view URL] script accordingly 3. prove it works with a series of long and short 3gp, wav, avi input files 4. ensure the best possible performance (CPU/run time for conversion) for given memory 5. tell us how to adapt the options in order to perform the following in future: a) limit the length to a maximum length b) 6. a Flash player should be able to run the mp4, stop, play again, move forward, and back. We would give you access to our backend and point you to the required folders. This is for developers with experience in ffpmeg and mp4.