I use three presets for the Video module: mp4, webm, and ogv, each of which functions normally on its own in supported browsers. (I'm on Mac OS X 10.6 and 10.7 and using Chrome, Safari, Firefox, Opera, and Camino. IE 9 doesn't play webm either on Windows Server 2008R2.)
What I'm able to verify now is that some transcoding jobs are passed through while others are not — even though the files work in some browsers. Transcoding results from a Nikon D4 (H.264) to a Video preset for mp4 doesn't work at all in Chrome, while it works great in Safari.
BUT if I convert that file to ProRes 422 and then transcode using the same presets, Chrome will display it.
If I show source and click on the mp4 file it hangs; but when I click on the webm or ogv files themselves, they both play. Webm has the best performance and starts immediately, whereas ogv needs to finish loading before it will play.
I have actually seen some of these newly transcoded mp4 files play in what looks like a QuickTime wrapper, but I can't reproduced that at the moment.
[EDIT: links deleted]