How do I use ffmpeg to merge all audio streams (in a video file) into one audio channel?

You can use ffprobe to find the number of audio streams and use the output as a variable in your ffmpeg command. Bash example using wc to count the audio streams listed by ffprobe:

ffmpeg -i input.mov -filter_complex "[0:v]scale=-2:720,format=yuv420p[v];[0:a]amerge=inputs=$(ffprobe -loglevel error -select_streams a -show_entries stream=codec_type -of csv=p=0 input.mov | wc -l)[a]" -map "[v]" -map "[a]" -c:v libx264 -crf 23 -preset medium -c:a libmp3lame -ar 44100 -ac 2 output.mov

The following command should do the same thing as llogan's answer but doesn't recompress the video track and requires you to identify how many audio tracks should be merged together.

If you want to know how many audio streams are present, try:

ffprobe originalfile.mov 2>&1 | grep 'Stream #'

Once you have identified how many audio streams should be merged, use that number in the amerge=inputs=2 parameter here. This command will merge the streams into one and recompress the audio using aac compression.

ffmpeg -i originalfile.mov -c:v copy -c:a aac -b:a 160k -ac 2 -filter_complex amerge=inputs=2 output.mp4