An interesting consideration when it comes to gravity is for spacecraft that are meant to operate planetside as well as in space. Planetside, a layout like a modern airplane (long and short) makes sense, whereas in space, a layout like a tall tower (tall and skinny) makes sense, provided constant - or at least frequent - thrust.
The Savage Chicken from the webcomic
Freefall has an interesting compromise - many of the amenities rotate or are otherwise setup to work under either situation. For example, the tables have booth-style seating, and the seats are setup so that the seat and back are functionally interchangeable, while the table can rotate for either orientation. That example can be see
here.
Another consideration - the bridge being located at the front of the ship, with a big transparent "window" to see out of. That's fine for a "spaceship" that's going to spend most of its time flying around planetside (such as for
The Savage Chicken), but realistically the bridge being further in, and relying on the ship's sensors, makes a lot more sense (using
Spaceships, a Control Room in one of the Core sections is going to be much more well-protected than one elsewhere, although I think ejecting your Control Room in an emergency isn't available if you do that). Things in space are, quite frankly, too far away for the human eye to be of any use - and given the velocities necessary to get anywhere, by they time you
can see something, it's too late for you to do anything about it. Best to avoid a big honking weakspot (transparent materials are unlikely to be as resilient as opaque ones) that doesn't even accomplish anything for you. Luxury spacecraft and the like, however, may well have direct viewports, for those wanting to see space with their own eyes rather than through a camera.