The Wikipedia page Interstellar Travel and the blog posting Spaceship Design 101 and its commentary are good places to start. Engines, radiation protection, heat dissipation, and life support seem to be the primary factors driving (real life) designs. Each factor helping to solve problems with the others: An annealed solution. But I still want cool models!
The web has a huge amount of creative work in this area being shared. If you look on Deviant Art or Pinterest for spacecraft you will find far more than you can reasonably review, especially without a plan. My current plan is to pick a rule set's ship design section and then using the point values for ship capabilities & capacities determine a visual volume of their sizes. For example, Warcosm has the following sized ships:
I have then used this to calculate volumes with the proportions of length × width × height = 5n × 2n × 1n. I then use 123D Design to look at them and make an esthetic judgement about the relationships between the ships at high and low point size. For example, here are a horizontal and vertical Dreadnought next to a Cruiser and a Pinnace.
The question now is do the size differences look right?