What are the most popular and freely commercially distributable video codecs?
H264 AVC, H264 , WMV and other popular ones are not free to distribute in commercial products.
ADDED: Is there any quality difference between H264 and OGG Theora?
There aren't many. Video codecs are almost all encumbered by IP problems. Ogg Theora is the only one that comes to mind. Theoretically XVid is as well, but that's based on MPEG4 and so probably has latent IP issues.
The only other solution is to go back to something old like MPEG1 which probably has lost most if not all of its patent protection by now.
Your question seems to be about container formats. MKV is not patent-encumbered. As Steven Rowe says, an MKV file using Theora for video and Vorbis for audio would be completely Free Software.