So in summary: be careful some software and technologies you use have licences that you should read.
If you are using any technology for commercial use you should probably be reading all licensing agreements and have your lawyers deal with anything that arises.
Or, just drop these technologies and use their free competitors (e.g. Theora) that don't require you to engage your lawyers just to compress some videos.
But there are no barriers to adopting Theora practically overnight, once the market expresses an interest. Vorbis seems to be well supported after an initial wait-and-see period.
And what if you have around 8 petabytes of video (http://beerpla.net/2008/08/14/how-to-find-out-the-number-of-...) in H.264? What would you do, double your storage? How long would that take to re-encode anyways. The reason why Youtube is using H.264 instead of Theora is because they already have the videos in that format.
Here’s hoping for the dream scenario: Google release VP8 as a open and free format with a patent indemnity clause, then migrate YouTube over to it. They also release open specifications for a VP8 hardware decoding part, an OpenCL codec, and help Adobe bundle support into Flash for Microsoft and Apple browsers.
We learned in Betamax vs. VHS that there are risks involved in backing an emerging format. The difference here is that it's a little easier for different codecs to coexist, even with varying licenses. The problem is that publishing shouldn't be limited to big players that can afford expensive and restrictive licensing agreements. There has to be a solution for the everyman, nonprofit, and nonprofessional. An unencumbered, nonrestrictive and free codec has to be an option, and Theora is one possiblility, if it can be easily supported in a product without worrying about licensing issues.
On the iPhone, they can't. On the desktop, it's more likely that they'll click the back button than download a codec, install it, relaunch their browser and navigate back to your site.
If you are using any technology for commercial use you should probably be reading all licensing agreements and have your lawyers deal with anything that arises.