I am currently focusing my worldbuilding efforts in designing a story (or, perhaps, if all goes well, a series of stories) that take place in space.
In my constructed reality, there exists a material with metaphyisical origins (which is quite a bit of handwaving, I know...) that isn't comprised by atoms, instead being completely solid (I know, I know, completely stupid and completely impossible by our current knowledge of Physics, but...). Furthermore, it also has no mass (so no inertia) and isolates whatever may be inside from all forms of radiation and direct impact. Let us call it, quite appropriately, handwavium.
So, with this handwavium, as well as with the (once again, handwaved) possibility of extracting zero-point energy or some other law-defying solution like that, as well as FTL travel, one should not have, at least as far as I can tell, any kind of restraints in designing the ships.
And that brings me to the question: assuming the ships should be primarily space-borne (with the possibility of landing on planets if desired/needed), with the intent of acting as the headquarters of some kind of well-intentioned organization (so, with the capability to hold about a thousand to ten thousand people in comfortable lodgings, with all kinds of technological goodies), what should be their shape?
Oh, I almost forgot, there is a way to create handwavium in any shape we want, and the way it is made implies that the surface is completely smooth, so, in principle, there should be no friction (from fluids flowing alongside the surface; of course that entering an atmosphere with a straight surface should cause resistance...). There are also ways to artificially generate gravity and annulate the inertia of the passengers, so that is not a concern.