I created a Windows batch file to re-encode all videos in a directory. Just install Handbrake to the default directory and then drag and drop the video directory onto the .bat (or create a SendTo link to the .bat) and it will do the magic for you. 400k/s video and 64k/s audio works fine for most videos but you can edit the file if you care a little less about space.
Edit: Make sure the path to the video folder contains no spaces. Even though the quotes should make it work properly it throws an error if there are.
Edit: Updated for non-.mp4 extension files
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