Where to start.
Let's start with your links:
The guy admits that he is disappointed by Theora, it was annihilated by x264.
I only went through it quickly but the guy uses Sorenson Squeeze, not even on the map in terms of H.264, at least use a decent encoder like x264. Even then Theora still lost, LOL, Theora has no future.
This article talks about the Peak signal-to-noise ratio (PSNR), those values are of little relevance in reality, it's something used by the people working on encoders. You can easily tweak a encoder for a brilliant PSNR, that doesn't mean it'll look good (in fact it won't look good at all). Do your research, PSNR is not a quality measure. EDIT: I see even the author on /. says the same thing. Regardless x264 added an option recently to drastically improve the PSNR, decreases image quality tho (as if there aren't enough independent research and information that proves PSNR is a useless measure for quality).
This is probably the most respected video encoder shootout, extensive information on the methodology and extensive testing:
http://compression.ru/video/codec_comparison/h264_2010
Notice how Theora is even obliterated by MPEG-4 ASP (in that case XVid), came dead last in the comparison, x264 and MainConcept tied in first place. Once again, x264 is open source and freeware. It's is arguable the best H.264 encoder around and you don't have to pay to use it. Libavcodec decodes H.264 and it's freeware and open source, there are other freeware open source decoders also. Remind me why H.264 is bad again? Standard and patents are only a problem if you actually have to pay a fee. As I said, so far as I know it's free so long as the software is free.
Theora isn't widely adopted, in fact the opposite, and it never will be because no mayor companies are pushing it. You have to have the right company to back a product. H.264 is supported widely in both hardware and software, Theora, has 1 or 2 codecs that support it.
@Gnome: The only HTML5 specific tags used in that demo are <audio> and <video>. Nothing special - Firefox and Chrome are supporting the OSS codecs (Ogg, etc.) as opposed to the H.264 codec (which both Microsoft and Apple have their muddy fingers in selling to the world). Besides that, they use vendor sniffing to block out the modern browsers. That's bad marketing, and it's coming back to bite them already. Check the blogosphere on this story.
Microsoft uses VC-1, Apple uses MPEG-4 AVC (AKA. H.264), not the same thing, not even close. VC-1 is the only real competitor in terms of image quality to H.264 and there are no open source solutions and I doubt there ever will be, knowing MS.
As I said I have no comments on the HTML part, I was simply commenting on the video codec, I don't care for Apple or MS and what they think they'll impose in terms of the HTML 5 specification, I'm simply pointing out the facts regarding video encoding. I've been heavily involved in video coding and I can confidently state that the best choice is H.264, VC-1 is too proprietary and Theora has a plethora of problems.