I am an advocate of open-source codecs such as Theora and Vorbis.
Many people though prefer to use other codecs and containers.
This is necessary when uploading files to YouTube.
I don't expect RecordMyDesktop to offer other codecs when converting, but I think it would be a great advantage if there was the choice "Convert or Raw?".
If the user were allowed to choose 'Raw' then he can easily convert later using any codecs and file types with some other program.