channelAustin has been using a proprietary software tool called Content Agent to encode .mov files to the MPEG2 format required for playback on our Synergy Broadcast system. Content Agent in our work flow has been previously discussed. See http://groups.drupal.org/node/19135
We also decided some time ago to use Content Agent to encode H.264 files for VOD on the web with the OM Show module. And so we added an H.264 encode process to the workflow. We've now decided to stop doing that.
We're realizing the Content Agent is not as robust as we thought. The near simultaneous encoding of both MPEG2 and H.264 files puts too much demand on processes on the CA machine. We've had a number of issues and problems related to this.
So we are investigating other ways to encode to H.264. We're looking into Handbrake. And we're looking into something based on Handbrake called DropFolders. http://ctl.du.edu/staff/josephlabrecque/DropFolders/
We've also had trouble communicating between our web server and the Edit Share system. We've decided to send encoded H.264 files directly to a drive on the web server.
Point is we are re-configuring the work flow for both how we encode H.264 files and where those H.264 live. I suppose this is part of the learning process in developing this system.

Comments
I doubt this helps
I doubt this helps you, but we're moving all encoding over to Archive.org and suggesting that as the default workflow for the Open Media Project. At DOM (and anywhere with sufficient bandwidth), its a superior workflow than using our previous solutions (First we were using a ProCoder solution that TelVue helped us set up, then moved to an FFMPEG solution we built internally). Both of those systems required more upkeep and intervention than just sending the raw files to Archive.org. With the OMP Collection, they encode an Mp4, an ogg file, and an Mpeg2 following the ACM Server Standards Working Group guidelines. All our VOD is streamed directly from Archive.org.
THe only down-side to this approach is 1. it requires a strong internet connection, preferably internet-2, and 2. It requires creative commons (since its designed to enable content-sharing between stations, in addition to reducing encoding and VOD costs for users.
We'll be doing some work this summer for MediaBridges, who has a rather slow internet connection, so we will likely need to try something else with them, and it'll be helpful to see what you're doing and if you find an affordable and manageable internal solution.
Tony
Whatever your first issue of concern, media had better be your second, because without change in the media, the chances of progress in your primary area are far less likely. http://denveropenmedia.org