Jarrod, Right at this moment I am transcoding ex-m2ts files from my own HD camcorder to mpg2; very good mpg2 as it happens. For that I am using TMPGEnc 'Video Mastering Works 5', for the use of the very good codecs it has. Another advantage, is that once you have committed your transcoding to 'batch' processing, there seems to be no reason not to switch-off, then restart the parent programme, and get at least partway through teeing-up the next project to save time later.
Although I am reluctant to run anything CPU or RAM-intensive while transcoding as well, it seems to do no harm to carry the next incoming process partway through, eg loading and numbering the clips ready for trimming to length and other processing after the batch processes are completed. 'Panasonic' provided me with software to do this job on the DVD which accompanied my camcorder, but TMPGEnc does it better. I put that down to the fact that I am able to run the TMPGEnc software somewhat slower, whereas, with the supplied software, quality may have been sacrificed to speed, to a certain extent.
And, 'Avidemux'? I've used it a bit and it works well, however, it wouldn't permit me to use 'Muksun 2.1' my favourite de-interlace, since all 'filters' in 'Avidemux' are in the form of *.dll, and Muksun' is a 'vdf' files as with 'Virtualdub', so there is no 'carry-over'.