If you are using graphedit... to avoid the asf thing, choose in the drop box "All files"... i dunno why it does that !
You think it's bad to mix writer and muxer in one ?
I will probably create a filter with an output in the future because you may want to output that over a network instead of a file for example.
The skeleton of the theora encoder went into xiph svn tonight... but i haven't filled it in yet... there's still a problem with wmp9 and the theora decoder... it needs a bit of a rewrite to fix
The version in svn... has fixed most of the muxing bugs, and accepts multiply input streams.
I have exams starting... so it may or may not get done soon !