well it depends.
you can get;
-wifi card purchased and installed
-graphics card upgrade
-hard drive upgrade (some usually just have the 500GB models) not always.(newegg is better for this anyway)
-Ram installation/upgrade (though newegg and owc is better for this)
the only other options that may not be custom configed in the store is the wireless mouse and keyboard, maybe...depends on the store.
i have had colleagues custom configure a bunch of components with their macpros in the past since they needed it instantly.
id call ahead and see if you can get a shopping appointment.
(otherwise they could have you pay by 'cheque' at the store and they do the order from within.)