Like what? how do you make ships that look different from eachother but also recognisable to one game? especially if you use many different designers.
What a strange question.
Star Trek: Federation vs Klingon vs Romulan vs Gorn vs Cardassians vs Borg (and the list goes on and on)
Elite: Fed vs Empire vs Alliance (and independent ships). Even the cheese wedge shapes make the ships distinctly Elite in style.
Homeworld: Vaygar vs Hiilgaran
X series of games: Boron, Split, Paranid, etc.
Its not hard when you have someone laying down art direction for the artists to follow. This race's ships are like this. This race's ships are like this.
Most SC ships scream generic sci-fi.
Ok, its not totally a bad thing. Familiarity can actually help people feel comfortable with the designs. It might even get them fans "Wow, this ship looks so much like the ship from Firefly!" (or whatever).