My personal preference is to return the return value, rather than using a reference; more generally I like to avoid my functions having side effects because they make the function trickier to analyse (for example, using references make functions more difficult to refactor out because you need to send the reference with it and bring the changed values back again - using pass-by-value semantics means the sending and bringing are built in).
To the extent that I tend to have things like
function sortBy($array, $comparator)
{
usort($array, $comparator);
return $array;
}
I just like being able to write
filter(sortBy($foo, $sortfn), $filterfn)
without worrying about side-effects or having pass-by-reference warnings.