Two work flow apps that I have begun to use to track my work are Workflowy for tasks that I need to get done and Azendoo for tasks that I need a group of people to get done. Both are appropriate for middle school students, though they will need to create accounts.
Workflowy is great for the person who finds himself/herself writing out lists of things to do at home and at work. Keep them both in the same place and then embed lists within lists. Does this sound like a Type A person's dream come true? It is! Sync between your computer and phone. Get daily updates on what you've done and what you still have to do. Watch the demo video below, sign up and start making lists.
As for Azendoo, here is a great way to break up group projects into small tasks assigned to specific group members. You can set due dates, sync with other mobile devices, and link work to apps like Evernote, Dropbox and Google Docs. All parties can be held accountable and work becomes transparent when everyone is working via collaborate apps. To learn more about how you and/or your students can use Azendoo effectively, visit the help page for answers to your questions. To get a visual sense of how this software can be helpful, watch the promo video below. Other tutorials exist on YouTube.