<?PHP
//create array of pairs of x and y values
$dataset1 = array();
while ($row = MysqL_fetch_assoc()) { //or whatever
    $dataset1[] = array( $row['xvalue'],$row['yvalue'] );
}
?>

<script type="text/javascript">
    //put array into javascript variable
    var dataset1 = <?PHP echo json_encode($dataset1); ?>;

    //plot
    $(function () {
         $.plot($("#placeholder"),[ dataset1 ]);
    });
</script>