The order of the extensions influence the velocity of the reply. For example: 

spl_autoload_extensions(".php, .inc");

is more fast than:

spl_autoload_extensions(".inc, .php");

Check out this example:

Some class files:

ClassA.php
<?php class ClassA { var $val = 'Hello from class "ClassA"'; } ?>
ClassB.php
<?php class ClassB { var $val = 'Hello from class "ClassB"'; } ?>
ClassC.php
<?php class ClassC { var $val = 'Hello from class "ClassC"'; } ?>
ClassD.php
<?php class ClassD { var $val = 'Hello from class "ClassD"'; } ?>
ClassE.php
<?php class ClassE { var $val = 'Hello from class "ClassE"'; } ?>

1. Simple:
<?php
// default priority: .inc .php
for($n=65; $n<70; $n++) {
    $className = 'Class'.chr($n);
    spl_autoload($className);
    $ins = new $className;
    echo $ins->val.'<br>';
}
// 4.2 miliseconds
?>

2. Change priority:
<?php
spl_autoload_extensions('.php,.inc');
// new priority: .php .inc
for($n=65; $n<70; $n++) {
    $className = 'Class'.chr($n);
    spl_autoload($className);
    $ins = new $className;
    echo $ins->val.'<br>';
}
// 1.4 miliseconds
?>

Extensions doesn't have to start with a dot, spl_autload() will simply append whatever you supply to the basename. The following example will try to load "test.php" first, and "test/index.php" as well:

spl_autoload_register('.php,/index.php');
spl_autoload('Test');