In this case, the submarine patents surround Ogg Theora is my biggest issue what I was implying more than anything else. The W3C is looking for an (HTML5) audio/video that's open, universally available and doesn't seem to be laden with patents that will stop integration into certain products.

Ogg Theora cannot say that. But to answer your question, Ogg Theora is based on a proprietary VP3 codec. That means that despite being open, it's a fork of what people would know/use and thus different and comes with certain limitations and/or workarounds that exist for a multitude of reasons. But it still makes it proprietary. That's what I meant.

Hope this answers your inquiry. And I state it all as opinion, not fact.