I can remember reading some commentary in exobiology articles about two things:
1) It's hardly likely that humanoid species exist for if evolution happens on another planet, then it's hardly likely that the same conditions would happen, and in the same order, such that a recognizable humanoid species would emerge.
That likely would result in very strange looking starships to fit the needs of the species using that ship for interstellar travel, but might include some common components on the spaceship itself regarding life support, engines, shielding, and weapons.
2) It might be that humanoid species would be the most common because of unknown scientific laws. In other words there was a natural order to evolution such that the apex predator would become a bipedal species with common sense organs and means of procreation, digestion, circulation, respiration, etc.
In that case, those humanoid species might develop engineered structures for interstellar travel which were very similar.
From a production standpoint in the old days, having lots of noncorporeal beings was a challenge such that the viewers could identify with such an alien. Communication with such a being could exist from a mathematical method only as the constructs of language rely upon a mouth and tongue. Instead it could be periods of emmitted light.
Now with CGI, there really aren't those constraints, but it's still very expensive.
One of the things that most impressed me about the actors of Star Trek was how little they saw of the graphic elements until way after shooting the episode. Imagine staring at a blank surface and trying to convey excitement, fear, awe, etc when there's nothing for your eye to see.
I liked the geometric shapes of the Borg vessels which skipped any aerodynamic elements because they weren't intended for landing upon planets. That was just an amalgam of all of the assimilated species with precious little in terms of aesthetics because it was strictly utilitarian.
The aquatic Xindi vessels would have to be enormously strong because of the mass of water carried within the hulls. One noncorporal species had a huge ship, but it wasn't clear how they acquired it, or why they would need it, though it was stated they couldn't live within the vacuum of space. Star Trek Enterprise "The Crossing" was that particular episode.
A little side note that's relevant to the discussion. The original "saucer" comment by Kenneth Arnold was taken out of context. He was describing the way it skipped like a stone across water, not the shape of the UFO he witnessed. A little known fact is that this image was taken by surveillance craft of an unknown craft about the time of the Roswell Incident in 1947. Looking for the photo for inclusion with this post. If I find it, I'll edit the post.
EDIT: Here's one of three known photos of a UFO within the same time frame (within days perhaps hours of the Roswell Incident).
EDIT2: Other photos from that time window:
Here's the actual rendering by Arnold which agrees with the real photo and makes the story far more compelling.
EDIT3: The earliest drawing submitted by Arnold which is slighly different than the artist's rendering for his book.
The mentioning of a saucer then influenced countless films in the midst of the contactee boom (a subset of the UFO phenomena different than other more scientifically inclined groups like NICAP). Some of these reports mentioned saucer shaped craft, but also cylindrical, airship-like craft dating back to 1897, the vimana of India from ancient times which were more like modern airplanes, and all manner of shapes included in the Condon Report.
Here's a similar collection of ship types (but not the actual Condon Report graphic which others may find illuminating for influencing the ships of Star Trek).
) alien influence. Then again, maybe one of the founding races of the Federation that we haven't seen ARE the "little green men" that abduct people to put stuff in their butts and turn cows inside out, so that influence is from them, after all. 
