<?php
$yourArray=array("4.0.1","trunk","branch","4.1.0","4.0.3");

function isVersion($a) { return is_numeric( str_replace('.', '', $a) ); };
function sortFunction($a, $b) { 
    if( isVersion($a) && isVersion($b) ) { 
        return version_compare($b, $a); // reversed for your proper ordering
    } elseif( isVersion($a) ) { 
        return -1;
    } elseif( isVersion($b) ) { 
        return 1;
    } else { 
        return strcasecmp($a, $b);
    }
};

usort($yourArray, 'sortFunction');

var_dump($yourArray);
?>