You can choose device specific presets to let the application choose automatically the appropriate output format.
Transmageddon allows you to convert from and to the following formats:
You can also choose to basically export the audio from a video file and also rotate the video for 90 or 180 degrees, or flip it horizontally or vertically.
Note that in order to use the latest Transmageddon version, you will need to install the latest GStreamer 0.11. Source