Spaceship Design: What makes sense, and what's nonsense?

[FF_Ninja]

I'm going to be spending some time in Inkscape and GIMP over the next few days working on some custom top-down spaceship layouts for use in a campaign later. In preparation for this, I started looking today for reference models (starting with my old stomping grounds, CGSociety).

It then ocurred to me that I'm highly influenced by sensational, flashy, exotic designs - and I don't have a clue what's more functional and realistic versus what might be highly improbably or unlikely a design feature to be incorporated.

To give you a point of reference: I don't see any functional or physical inconsistencies or design flaws with the typical Star Trek and Star Wars faire.

My plan is to design an entire hierarchy of new ships for futuristic Earth, starting from the earliest space-fairing vessels, gradually incorporating FTL into the design (haven't settled on what FTL actually looks like in this setting), and building on that form factor over time.

I would very much prefer to approach my designs with a practical understanding of what "would" and "wouldn't" make sense, rather than throwing elements together in an arbitrary fashion.

For those of you who consider yourselves more of an authority on "space-y" things, I would appreciate any insight into what would make sense in terms of spaceship design and form, and I appreciate any commentary on examples in media that stand out in one way or another.

Thank you all very kindly.