Using ffmpeg to copy metadata from one file to another

Use -map_metadata.

In this example the global and stream metadata will be copied from in0.mkv. The video and audio streams will be stream copied from in1.mkv:

ffmpeg -i in0.mkv -i in1.mkv -map 1 -c copy \
# copies all global metadata from in0.mkv to out.mkv  
-map_metadata 0 \
# copies video stream metadata from in0.mkv to out.mkv
-map_metadata:s:v 0:s:v \
# copies audio stream metadata from in0.mkv to out.mkv
-map_metadata:s:a 0:s:a \
out.mkv

This will result in something like:

Output #0, matroska, to 'out.mkv':
  Metadata:
    title           : Global Title
    AUTHOR          : Global Author
    Stream #0:0: Video: h264
    Metadata:
      title           : Stream 0 Title
    Stream #0:1: Audio: vorbis
    Metadata:
      title           : Stream 1 Title

By default global metadata is copied from the first input file, so -map_metadata 0 could probably be omitted.

From the comment in the answer How to make Handbrake preserve capture time / creation time?

A full command line adding the option to copy special tags will be:

ffmpeg -i in.mp4 -i out.mp4 -map 1 -map_metadata 0 -c copy -movflags use_metadata_tags fixed.mp4

For decoding Flac to AIFF whilst preserving metadata, this answer worked better for me: Covert FLAC to AIFF while saving tags/metadata

When using ffmpeg at a file which has metadata (like a title) in its streams, you need to use -map_metadata again, as it will not hold those metadata in the new output