For the Federations' technological development, and how they designed said technology, the 'saucer' shape was the best shape and fit for them for the best warp field. Each race is different in how they invented their technology and how they wanted to use it, regardless of the same basic principles, such as warp fields.
Zephram Cochrane first's ship (the Phoenix as shown in First Contact) wasn't saucer shaped at all, and in fact was an old nuclear missile body but it still worked for his purposes. As the Federation developed the warp coils and inertial dampeners and ect ect.. they discovered that the saucer shape was the best fit for their technology and provided the best results in using that technology.
Obviously, other races developed their own technology but it is similiar in most regards. But, in how they developed their technology also influenced their ship-building. Also, other factors, like building materials, metal composition, and placement of warp coils also affect the shape and integrity of the warp field.
As technology progresses, the Federation is slowly moving away from predominately saucer themed ships. The Prometheus, Defiant, and the Norway designs immediately spring to mind.
Now, technical explanation aside.. (Which is just my own opinion, though based on Star Trek technical manuals and my own observations watching the shows) The Saucer shape is the most predominant visual image of anything alien or really, space related of all time. Going all the way back to H.G. Wells and such. Gene Roddenberry, most likely used it in his ship designs to pay homage to all the great science fiction that came before him. But again, that's just my opinion.
