if your dates are not before 1970, I'd convert to unix timestamp to get the difference in seconds:
SELECT UNIX_TIMESTAMP(date1)-UNIX_TIMESTAMP(date2) AS time_diff FROM table
and use php to convert to hours, minutes and seconds:
$hours = floor($row['time_diff']/3600);
$minutes = floor(($row['time_diff']%3600)/60);
$seconds = $row['time_diff']%60;
echo $hours.":".$minutes.":".$seconds;
this isn't tested, but hopefully should give you the idea.