My organization is dealing with this problem right now.  We're going with Flash because we have to.  It's what most people use, it's a lot better than the hodgepodge of WMA, QT, and Real stuff that we've had, and you can't get fired for doing what YouTube is doing.<p>However, I did insist on H.264 flash videos in an MP4 container (rather than using VP6 in an FLV or something else).  That way, we can easily serve HTML5 video to Safari and Chrome as a straight MP4 file if we so choose in the future.  It doesn't help us with supporting Firefox/Ogg/a truly open standard, but it does mean that we can support Flash and HTML5/MP4 off of one file.  I truly hope that Theora takes off.  I hope even more that Google open sources VP8.<p>I just wanted to point out that one could serve video to both Flash and the iPhone/iPad off of one file with current technology.