For added BatchDPG fun with MKV, use MKVextractGUI to pull out what tracks you want (audio, video, subtitle) and put them in the respective fields in BatchDPG.
This one is pay but its cracked, but i doubt you care.
Riverpast Video cleaner. http://www.badongo.net/file/2425487
(DO DONT USE DEFAULT AVI CODEC!, the default avi codecs are set for windows media player so the avi videos will be over 4-10gbs since the encoder is so outdated use a newer one), when using riverpast dont forget to enable codecs when encoding to avi or other formats (i usually encode mkv to divx with subtitles).