stereo + stereo → stereo
Normal downmix
Use the amix filter:
ffmpeg -i input0.mp3 -i input1.mp3 -filter_complex amix=inputs=2:duration=longest output.mp3
Or the amerge filter:
ffmpeg -i input0.mp3 -i input1.mp3 -filter_complex amerge=inputs=2 -ac 2 output.mp3
Downmix each input into specific output channel
Use the amerge and pan filters:
ffmpeg -i input0.mp3 -i input1.mp3 -filter_complex "amerge=inputs=2,pan=stereo|c0<c0+c1|c1<c2+c3" output.mp3
mono + mono → stereo
Use the join filter:
ffmpeg -i input0.mp3 -i input1.mp3 -filter_complex join=inputs=2:channel_layout=stereo output.mp3
Or amerge:
ffmpeg -i input0.mp3 -i input1.mp3 -filter_complex amerge=inputs=2 output.mp3
mono + mono → mono
Use the amix filter:
ffmpeg -i input0.mp3 -i input1.mp3 -filter_complex amix=inputs=2:duration=longest output.mp3
More info and examples
See FFmpeg Wiki: Audio Channels