$sql = "SELECT
    s.Title AS Subject,
    s.Subject_ID AS Subject_ID,
    c.Title AS Course,
    c.Course_ID AS Course_ID
    FROM
    subjects s
    LEFT JOIN courses c ON s.Subject_ID = c.Subject_ID
    WHERE s.Faculty_ID = $faculty";

$res = mysql_query( $sql );
while ( $row = mysql_fetch_assoc( $res ) ) {
    $return[$row["Subject_ID"]][] = array( "Course_ID" => $row["Course_ID"], "Title" => $row["Course"] );
}

print_r( $return );

switch($_GET["cmd"]) {
    case "populateForm" :
        $return = json_encode( populateForm() );
        break;
    case "populateCourses" :
        $return = json_encode( populateCourses( $_GET["faculty"] ) );
        break;
}

echo $return;

function populateCourses( $faculty ) {
    $sql = "SELECT
        s.Title AS Subject,
        s.Subject_ID AS Subject_ID,
        c.Title AS Course,
        c.Course_ID AS Course_ID
        FROM
        subjects s
        LEFT JOIN courses c ON s.Subject_ID = c.Subject_ID
        WHERE s.Faculty_ID = $faculty";
    $res = mysql_query( $sql );
    while ( $row = mysql_fetch_assoc( $res ) ) {
        $return[$row["Subject_ID"]][] = array( "Course_ID" => $row["Course_ID"], "Title" => $row["Course"] );
    }

    return $return;
}

Array
(
    [8] => Array
        (
            [0] => Array
                (
                    [Course_ID] => 59
                    [Title] => Core ICT
                )

            [1] => Array
                (
                    [Course_ID] => 60
                    [Title] => BTEC Business
                )

            [2] => Array
                (
                    [Course_ID] => 61
                    [Title] => BTEC ICT
                )

            [3] => Array
                (
                    [Course_ID] => 62
                    [Title] => GCSE Business
                )

            [4] => Array
                (
                    [Course_ID] => 63
                    [Title] => GCSE ICT
                )

        )

    [9] => Array
        (
            [0] => Array
                (
                    [Course_ID] => 64
                    [Title] => Advance BTEC Business
                )

            [1] => Array
                (
                    [Course_ID] => 65
                    [Title] => Advance BTEC ICT
                )

            [2] => Array
                (
                    [Course_ID] => 66
                    [Title] => AS Applied Business
                )

            [3] => Array
                (
                    [Course_ID] => 67
                    [Title] => AS Applied ICT
                )

            [4] => Array
                (
                    [Course_ID] => 68
                    [Title] => A2 Applied Business
                )

            [5] => Array
                (
                    [Course_ID] => 69
                    [Title] => A2 Applied ICT
                )

            [6] => Array
                (
                    [Course_ID] => 70
                    [Title] => A2 Economics
                )

            [7] => Array
                (
                    [Course_ID] => 71
                    [Title] => A2 Law
                )

            [8] => Array
                (
                    [Course_ID] => 72
                    [Title] => GCSE Maths
                )

            [9] => Array
                (
                    [Course_ID] => 73
                    [Title] => Maths
                )

            [10] => Array
                (
                    [Course_ID] => 74
                    [Title] => AS Further Maths
                )

            [11] => Array
                (
                    [Course_ID] => 75
                    [Title] => AS Maths
                )

            [12] => Array
                (
                    [Course_ID] => 76
                    [Title] => GSE Maths Rs-Sit
                )

            [13] => Array
                (
                    [Course_ID] => 77
                    [Title] => A2 Further Maths
                )

            [14] => Array
                (
                    [Course_ID] => 78
                    [Title] => A2 Maths
                )

        )

)

$('#courses').on("click", "option", function(event) {
            var id = $(this).val();
            UWA.Data.getJson(Input.URL + '?cmd=populateCourses&faculty=' + id, Input.populateCourses);
        })
    }

Input.populateCourses = function(data) {
    $('#courses').empty();
    for (var i = 0; i < data.length; i++) {
        alert(data[i]);
        $('#courses').append('<optgroup label="' + data[i] + '>');
        for (var x = 0; x < data[i].length; x++) {
            $('#courses').append('<option value="' + data[i][x].Course_ID + '">' + data[i][x].Title + '</option>');
        }
        $('#courses').append('</optgroup>');
    }
}

Input.populateCourses = function(data) {
    $('#courses').empty();
    for (var i = 0; i < data.length; i++) {
        alert(data[i]);
        $('#courses').append('<optgroup label="' + data[i] + '>');
        for (var x = 0; x < data[i].length; x++) {
            $('#courses').append('<option value="' + data[i][x].Course_ID + '">' + data[i][x].Title + '</option>');
        }
        $('#courses').append('</optgroup>');
    }
}

Input.populateCourses = function(data) {
    var html = "";
    for (var i = 0; i < data.length; i++) {
        html += <optgroup label="' + data[i] + '>';
        for (var x = 0; x < data[i].length; x++) {
            html += '<option value="' + data[i][x].Course_ID + '">' + data[i][x].Title + '</option>';
        }
        html += '</optgroup>';
    }
    $('#courses').empty().html(html);
}

Input.populateCourses = function(data) {
    var $courses = $('#courses').empty();
    var $optgroup;
    for (var i = 0; i < data.length; i++) {
        $optgroup = $('<optgroup label="' + data[i] + '>').appendTo($courses);
        for (var x = 0; x < data[i].length; x++) {
            $('<option value="' + data[i][x].Course_ID + '">' + data[i][x].Title + '</option>').appendTo($optgroup);
        }
    }
}

Input.populateCourses = function(data) {
    $('#courses').empty();
    for (var i in data) {
        alert(data[i]);
        /*...*/
    }
}