Drupal queue task sequencing
Together with a bunch of other people we created the queue runner and it does support this use-case and we use it internally. You can add a collector task that includes all your small tasks and you add a second collector task so it is executed after the whole lot of small tasks. See the API file for the queue runner to figure out how you should do this exactly. It works with the default Drupal queue class so you can even extend it with external queue systems such as http://drupal.org/project/aws_sqs (amazon queue class) or others.

http://drupal.org/project/queue_runner Works for D6 and D7