Fortunately it is quite easy to use a combination of ffmpeg and Python Gimp-fu to exploit all of Gimp's capabilities for batch processing video clips frame by frame. Here is a small example, where I applied Gimp's National Geographic Filter on a short clip. Depending on your system, you might need some patience, if you plan to process longer clips.
The scripts that were used to this can be found here. It is quite easy to modify it to use any other arbitrary set of Gimp filters, image processing operations, etc.
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