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Try:

find . \( -name '*.mkv' -o -name '*avi' -o -name '*mp4' -o -name '*flv' -o \
          -name '*ogg' -o -name '*mov' \) -exec sh -c '
  for file do
    target="${file%.*}.mkv"
    echo ffmpeg -i "$file" "$target"
  done' sh {} +

Replace echo with whatever command you want to use.