修改如下<SCRIPT LANGUAGE="JavaScript">
<!--
var sub_departmentid = new Array(); 
<?
while ($sub_result=mysql_fetch_array($stmt,MYSQL_BOTH))
{
  $sub_departmentid[]=$sub_result[departmentid];
  echo "ary_departmentid[".$sub_result[departmentid]."] = '".$sub_result[departmentid]."'"; //将php数组赋值给js数组
}?>
function  selectAll(department,all)  
{
alert(ary_departmentid); //打印js数组
}
//-->
</SCRIPT>
<?
foreach($sub_departmentid as $id)
{
echo "<td width='20'><input type='checkbox' name='chkdepart' value='$id' onclick=selectAll($id,this)></td>"; 
}
?>