For most applications that I work on, I include query profiling output that can easily be turned on in the development environment. This outputs the SQL, execution time, stack trace and a link to display explain output. It also highlights queries running longer than 1 second.
Although you probably don't need something as sophisticated, you can get a fairly good sense of run time of queries by writing a function in PHP that wraps the query execution, and store debug information on the session (or simply output it). For example:
function run_query($sql, $debug=false, $output=false) {
$start = microtime(true);
$q = mysql_query($sql);
$time = microtime(true) - $start;
if($debug) {
$debug = "$sql<br/>$time<br/><br/>";
if($output) {
print $debug;
} else {
$_SESSION['sql_debug'] .= $debug;
}
}
return $q;
}
That's just kind of a rough idea. You can tweak it however you want.
Hope that helps -