A two part piece of furniture where the top cabinet houses a telephone, pen, paper, and other muktzah goods, and the bottom is a cabinet containing nothing muktzah, but not any food or sephorim either, holds an item (in the lower cabinet) that one needs for Shabbos -- let's say paper napkins. The entire piece of furniture is a bassis, correct? Or can the napkins still be retrieved, for some reason?

As long as the furniture is not being moved,there should be no problem with removing the napkins

The bottom would be Basis for the things that are in the top (it’s considered one object.) but there is no reason not to take the napkins from the bottom if your not touching the cabinet. If the door of the cabinet is closed, you can open it using a different part of the body besides your hand or using an object (like a stick like utensil) to pry it open. (This is permitted when you’re moving it for a permissible thing (the napkins.) Moving with a part of the body there is a Machlokes if it’s permitted even to help the Muktzah thing.)

Even in the case you bring, the Muktzah objects you mention might not make it Bosis. Pens are utensils, though their prime use is for something that is forbidden, yet it’s permitted to be moved if you need to use it for a permitted use (At least when there is no other permitted utensil that can do that job) or if you need the place it’s put on. A telephone may also fall under this category. (This would depend on if it’s too delicate to use it for any other use than to talk on, because if it’s too delicate, then it’s completely Muktzah. If those objects are not totally Muktzah, then the cabinet is not Bosis (at least for the point of opening it and getting the napkins.)