I agree, Avidemux should have support for Ogg and Theora.
This has been reported upstream:
http://bugs.avidemux.org/index.php?do=details&task_id=427
** Changed in: avidemux (Ubuntu)
Importance: Undecided => Wishlist
Status: New => Triaged
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Ogg support for avidemux
https://bugs.launchpad.net/bugs/226163
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