You can try explicitly adding content type at the top of your file as below
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
and remove the below from your code..
header('Content-Type: text/html; charset=ISO-8859-9');
Update:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Untitled Document</title>
</head>
<body>
<?php echo "for example Ş and İ "; ?>
</body>
</html>
The above code gives me the below output: