If you need to unpack a signed short from big-endian or little-endian specifically, instead of machine-byte-order, you need only unpack it as the unsigned form, and then if the result is >= 2^15, subtract 2^16 from it.
And example would be:
<?php
$foo = unpack("n", $signedbigendianshort);
$foo = $foo[1];
if($foo >= pow(2, 15)) $foo -= pow(2, 16);
?>