In LEGO Star Wars: The Complete Saga you can unlock ships. What are they for? Where can I use them?
Ships are used in the various vehicle missions (pod-race, death star, battle of hoth) etc.
By unlocking them, you get to use them in these missions. Most of these missions have special "imperial" areas (marked by red and black gates) that only imperial ships can get through. Most (if not all) of the imperial ships are obtained by unlocking/purchasing them, so you'll want at least one to get 100% completion.
If you are referring to the minikit ships, you use them in the minikit "bonus" levels. Other than that they are just for completion and fun :).