Doctopus:
It now has a "Individual - Differentiated" option which allows individual assignments to be distributed by student "level."
It now allows whole class comment ability to be added to facilitate peer review.
It lets you distribute folders full of resources in addition to Documents, Presentations, Spreadsheets, and Drawings.
As of Doctopus 4.0 it now connects to a Chrome extension called "Goobric" which lets you associate a rubric with your Doctopus assignment and do rubric-based grading right in the top corner of your browser.