I friend of mine has just finished this tool. It's really great way to convert when you end up with director bringing you footage from mobile phones cameras camcorders vhs MTS, Blueray etc. With this thing, you can search the root folder or partition or disk and it will analyse it for most common formats. then you got the files sorted by their format. you can then apply output codec preset (which you make it yourself in ffmpeg(video) or sox(audio) or similar) and viola :) In destination folder, it RECREATES FOLDER STRUCTURE from the original source location. I used it on a making off documentary last month and it was really great. I had 20 hours of footage.. and to save time, I just did a proxy of everything in H.264 and gave tit to director. the director then watched it alone and prepared himself for editing without wasting time watching it again and again. Great stuff really. Free 30 Days fully functional trial.
I am seriously thinking of maybe possible integration with woowave as a good way to prepare files before syncing :), I'll let you know.