Since version 3.00 transmission now supports labels for torrents. They can be provided at add-time, see Sec. 3.4 of the RPC spec.

It would be neat if the transmission plugin accepted the labels keyword so Flexget could automatically label torrents., E.g. one could do

set:
    path: '/var/Downloads/{{series_name}}'
    label:
        - '{{series_name}}'
        - flexget