The OGG Vorbis Licence contains some provisions on patent licensing. On2, the owner of the patent, basically waive its rights to enforce the patent:
Here is what the LICENCE file in the libtheora-1.0 release says:
Please see the file COPYING for the copyright license for this software.
In addition to and irrespective of the copyright license associated
with this software, On2 Technologies, Inc. makes the following statement
regarding technology used in this software:
On2 represents and warrants that it shall not assert any rights
relating to infringement of On2's registered patents, nor initiate
any litigation asserting such rights, against any person who, or
entity which utilizes the On2 VP3 Codec Software, including any
use, distribution, and sale of said Software; which make changes,
modifications, and improvements in said Software; and to use,
distribute, and sell said changes as well as applications for other
fields of use.
This reference implementation is originally derived from the On2 VP3
Codec Software, and the Theora video format is essentially compatible
with the VP3 video format, consisting of a backward-compatible superset.
Now Theora is only a published specification, not a "standard" as such in itself.