One of the things we try to do is automate as much of the backend work as possible. We recently managed to automate our order entry into Quickbooks (i.e. the orders from our site download direct into QB - thus reducing the punch in time which was getting significant). We've also got shipping 90% automated, with only the packing and weighing of the boxes and box sizes being the last bits we have to do.
One thing we haven't done - which was brought to mind by 3 hours of work today - is the updating of stock levels. That is, when new stock comes in, we still have to manually edit each product to show the new stock quantities.