Divx Doctor II does batch conversions, but then you still need 3ivx to decode. There's some shareware ASS app on versiontracker called QTBatchExporter to let you batch convert to another codec, like Apple's MPEG-4. Or you could use a shell script to convert them to MPEG-1 with ffmpeg. The only other things I can think of are Media Cleaner and pasting them all together in QTPro and then re-splitting after the conversion