Hi Rich,
Unfortunately, Adobe Media Encoder doesn't have native support for ogg/theora or ogg/vorbis. However, you can install a (currently beta) plug-in on your system which will enable ogg encoding in AME:
Or, if you'd rather, you can also install the Firefox extension Firefogg, and encode to ogv directly from Firefox:
Firefogg - video and audio encoding for Firefox
I've had excellent results using both of the above methods.
hth,
Joe