Enabling debugging in Joomla! is great for seeing which SQL queries run, but I wanted to know which ones were taking the longest.  This is how I modified the core files to display runtimes:

.../libraries/joomla/database/database/mysql.php

function query()
{
	if (!is_resource($this->_resource)) {
		return false;
	}

	// Take a local copy so that we don't modify the original query and cause issues later
	$sql = $this->_sql;
	if ($this->_limit > 0 || $this->_offset > 0) {
		$sql .= ' LIMIT '.$this->_offset.', '.$this->_limit;
	}
	// MOVED ABOVE if/LOG SECTION
	$this->_errorNum = 0;
	$this->_errorMsg = '';
	$starttime = microtime(true); // ADDED
	$this->_cursor = mysql_query( $sql, $this->_resource );
	$endtime = microtime(true); // ADDED
	if ($this->_debug) {
		$this->_ticker++;
		// ADDED ALL THE timediff LOGIC
		$timediff = 1000000*($endtime - $starttime);
		if($timediff > 1000)
		{
			$timediff = "!!!!! ".$timediff;
		}
		$this->_log[] = "(".$timediff."): ".$sql;
		//$this->_log[] = $sql;
	}

	if (!$this->_cursor)
	{
		$this->_errorNum = mysql_errno( $this->_resource );
		$this->_errorMsg = mysql_error( $this->_resource )." SQL=$sql";

		if ($this->_debug) {
			JError::raiseError(500, 'JDatabaseMySQL::query: '.

				$this->_errorNum.' - '.$this->_errorMsg );

		}
		return false;
	}
	return $this->_cursor;
}

After making these changes, I now get the amount of time it takes the queries to run as well as the SQL.  Then I can search my page for "!!!!!" to find any queries that take longer than 1ms.

Hope this helps others.