How to add watermark to all video files in a folder? (Mac, mencoder, terminal)
You should be able to do it from the terminal with ffmpeg's overlay filter ... download prebuilt binaries or install with Homebrew if you don't have it already and the command would look something like this:

ffmpeg -i video.mp4 -i watermark.png -filter_complex 'overlay=10:10' outputname.mp4


That'll place watermark.png 10px in and 10px down from the top right corner ...