MySQL/PHP Seleccionar solo valores únicos de varias columnas y colocarlos en matrices separadas

Si desea mantenerlo como una instrucción SQL, entonces podría:

$sql = "
    SELECT DISTINCT 'make' as descr,make as val FROM items
    UNION
    SELECT DISTINCT 'model' as descr,model as val FROM items
    UNION
    SELECT DISTINCT 'year' as descr,year as val FROM items
    UNION
    SELECT DISTINCT 'month' as descr,month as val FROM items
    UNION
    SELECT DISTINCT 'day' as descr,day as val FROM items
    UNION
    SELECT DISTINCT 'hour' as descr,hour as val FROM items";

$result = @mysql_query($sql, $con) or die(mysql_error());

while($row = mysql_fetch_array($result)) {
    $make_array[$row['descr']][]=$row['val'];
}