The most commonly used pages vary depending upon the stage in the site's lifecycle that has been reached and who is accessing the Admin.
So early on focus will be on the configuration, modules, locations/taxes and localization menus. These tend to be used a lot duriong site development, but are then returned to infrequently thereafter.
Then there's a burst of activity in the catalog menus (where categories and attributes are defined and products are added). Store owners will typically return to this regularly thereafter to manage their product portfolio, run sales and put products on special. They may also use the gift cert/coupons menus, though not all do.
However, in a successful store most of the time will now be spent in the customers menu or looking at reports processing orders.
The miscellany of functions under the tools menu may be used at any time in a site's lifecycle.
Often site owners split responsibilities. They may have a developer who configures the site, and employees who process the orders. These people will have completely different usage profiles.
Finally, your design would need to take account of the Zen Cart's extensibility. There are a great many add-in modules that add extra functionality to these menus. Generally those extra functions are added because they are intended to be used, sometimes even replacing existing functions (e.g. Super Orders).
