I don't know of anything cheap that is Cleaner-like but I'd look into QuickTime Pro or FFMpegX for budget considerations and maybe w/some basic scripts you could get the automation you need. For apps that are like Cleaner (including the price point) there is Episode (by the Flip4Mac guys), Sorenson Squeeze, and Compressor (although not a bargain unless you'd use the rest of the Final Cut Studio 2 suite).
Lethal