The best — though least helpful — way to do this is not to use MP3 files as your source files. WAV, FLAC or M4A files don't have this problem.

MP3s aren't made up of fixed-rate samples, so cropping out a section of an arbitrary length will not work as you expect. Unless the encoder was smart (like lame), there will often be a gap at the start or end of the MP3 file's audio. I did a test with a sample 0.98s long (which is precisely 73½ CDDA frames, and many MP3 encoders use frames for minimum sample lengths). I then encoded the sample with three different MP3 encoders (lame, sox, and the ancient shine), then decoded those files with three decoders (lame, sox, and madplay). Here's how the sample lengths compare to the original:

 Enc.→Dec.          Length     Samples  CDDA Frames
 -----------------  ---------  -------  -----------
 shine→lame         0.95"      42095    71.5901
 shine→madplay      0.97"      42624    72.4898
 shine→sox          0.97"      42624    72.4898
 lame→lame          0.98"      43218    73.5000
*Original           0.98"      43218    73.5000
 sox→sox            0.99"      43776    74.4490
 sox→lame           1.01"      44399    75.5085
 lame→madplay       1.02"      44928    76.4082
 lame→sox           1.02"      44928    76.4082
 sox→madplay        1.02"      44928    76.4082

Only the file encoded and decoded by lame ended up the same length (mostly because lame inserts a length tag to correct for these too-short samples, and knows how to decode it). Everything encoded by sox ended up with a tiny gap, no matter what decoder I used. So joining the files will result in tiny clicks.

Your browser is likely mixing and overlapping the source files very slightly so you don't hear the clicks. Gapless playback is hard to do correctly.

You need to insert a silent track between each track as you specify them so you end up with something like:

sox track1.wav silence.wav track2.wav silence.wav ... output.wav 

You can do that manually (as above), or we can loop the current directory with an inline for-loop. Something like this should work:

sox -n -r 44100 -c 2 /tmp/silence.wav trim 0.0 2
sox $(for f in *.wav; do echo -n "$f /tmp/silence.wav "; done) output.wav

The silence-generator is stolen from here.

just change -M with -m

-M = merge
-m = mix

If all the files have the same parameters, like sample rate and number of channels, you still can't just catenate them. You have to strip away the WAV header.

It may be easiest to use an audio file manipulation utility like sox, which contains a method for catenating files. In fact, it does this by default. E.g. to combine three .wav files into one long one:

$ sox short1.wav short2.wav short3.wav long.wav

A loop will not arrange the files in the order you want. What you want is to sort the names, but treat them numerically. sort -n will do this.

Thus:

$ sox $(ls *.wav | sort -n) out.wav

If sox cannot handle that many files, we can break up the job like this:

$ ls *.wav | sort -n > script

Then we have a script file which looks like:

1.wav
2.wav
...
3999.wav
4000.wav
...
file7500.wav

We edit that to make several command lines:

# catenate about half the files to temp1.wav   
sox \
1.wav \
2.wav \
... \
3999.wav \
temp1.wav

# catenate the remainder to temp2.wav  
sox \
4000.wav \
... \
7500.wav \
temp2.wav

# catenate the two halves
sox temp1.wav temp2.wav out.wav ; rm temp1.wav temp2.wav

As the first editing step on the file list, you can use the vi command :%s/.*/& \\/ to add a backslash after every line.

You should be able to do something like:

sox short.ogg -p pad 0 6|sox - long.ogg output.ogg

-p option to sox is used for piping - basically, it tells sox to use stdout as the output. Using - as the input to the second sox is actually saying input is stdin (which happens to be the stdout of the previous sox, as we are piping with |). pad 0 6 tells pad 0 seconds at the beginning and 6 seconds at the end.

Hope this helps.

You can do it with one invocation of sox like this:

sox -m in1.mp3 in2.mp3 in3.mp3 out.mp3

If you want to combine this with the pad effect you need to be clearer about what you want.

You're almost there. The -v option can be applied to each input file, and for any of the combine methods. Set the scale factor in front of the file you want it applied to.

sox -n -r 44100 -b 16 s660.wav synth 20 sine 660 # a pure A
sox -n -r 44100 -b 16 s440.wav synth 20 sine 440 # a pure E

sox -m -v 0.4 s440.wav -v 0.9 s660.wav mix4-9.wav # an A5 with weight on the prime
sox -m -v 0.9 s440.wav -v 0.4 s660.wav mix9-4.wav # an A5 with weight on the fifth