In the GUI add a Transcode tab to the properties/preview box.

The tab lists all available devices and then has field for whether the file needs transcoding, to what format, and a button to add the file to a list of files to be transcoded.

EG

Code:
Movie1
------
Device       Transcode to    Transcode state     Start Transcode
--------------------------------------------------------------
Samsung B    MKV               Pending  (3 of 6)      
PS3             MP4               Complete
HTC             MP4               Not started          <Button>