Well the differences arnt something you are going to see in the specs.....
The E3's supposed to OC better. E6's are still good if you dont plan on OC, or OC very much. E6's also have a better memory controller as well from what I understand.
So if you plan to run stock, I say who cares. Overclocking, get an E3. I just recently bought one off these forums for $115 shipped.