Join many MP3, OGG, and FLAC files into one WAV or FLAC

Assuming you want to merge them alphabetically, by filename:

for f in ./*.{ogg,flac,mp3}; do echo "file '$f'" >> inputs.txt; done
ffmpeg -f concat -i inputs.txt output.wav

The for loop puts all the filenames in a file called inputs.txt, one-per-line, and the second one uses ffmpeg's concat demuxer to merge the files. It is possible to use printf instead of the loop like so:

printf "file '%s'\n" ./*.{ogg,flac,mp3} > inputs.txt

Assuming a modern shell, you can also use command substitution to do the whole thing in a single line.

ffmpeg -f concat -i <(printf "file '%s'\n" ./*.{ogg,flac,mp3}) output.wav

You can do this with ffmpeg and sox:

for i in *.mp3 *.ogg *.flac
do
  ffmpeg -i "$i" "$i.wav"
done

sox *.wav combined.wav

If you start with only lossless files, you can use use shntool:

shntool join *.flac

It seems that the Sound Juicer that comes with Ubuntu writes broken FLAC files, which result in no MD5 signature in the file. MAKE A COPY of the directory containing the files you want to concatenate, then run the script below.
echo fixing broken FLAC files
find . -type f|grep .flac$ |while read file
do
flac -f --decode "$file" -o temp.wav
flac -f -8 temp.wav -o "$file"
done
rm temp.wav

Then run
shntool join *.flac
as above.