Yeah I am looking to do similar except that I want to do flv to mp3 and keep the names exactly the same, but have a different extension. I've searched around and I have seen some scripts so that might be the way we have to go. If you find out how to do this please post it up.
Edit:
Just paste this into gedit and save as filename.sh (filename being whatever you want to call it) and place it in the same folder as the files you want to convert. Then right click the file go to properties and under permissions check the box that says make executable (there is a terminal command you can use to do this, but I don't remember off the top of my head). When this is done you can either do ./filename.sh in terminal or just double click filename.sh and choose run.
Code:
#!/bin/sh
for file in *.flv
do
ffmpeg -i "$file" "${file%.flv}.avi"
done
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