WHY ARE MOST ALIENS IN STAR TREK HUMANOID?
The Canon Answer:
In "The Chase," (TNG), it was revealed that an ancient race "seeded" planets with similar genetic material that would produce humanoid life.
The Lowdown:
Budgets. From as far back as TOS, Trek has had a limited budget to make aliens look alien, and while the budget has grown as time has passed (making way for unusual-looking humanoids like Morn, and CGI characters like Species 8472), there's still a limit to what the creative people can accomplish in a limited time.
We also have to keep in mind that in many stories, the "alienness" of an alien's appearance is only superficial...Trek is a series about ideas, and about the human condition, and sometimes that needs to be reinforced by having the aliens look not as alien, so we can identify with them as "human" characters and not be too distracted by unusual appearances...it's the same reason why most Trek adventures take place on "Class M" planets.
The Non-Canon Answer:
"The Chase" addressed this issue in a somewhat interesting way, and helps address the issue of interspecies procreation. But in the case of the proliferation of the humanoid form (walking erect on two legs, having two arms, opposable thumbs, a head on top of the torso containing the key sensory organs, having two eyes and two ears) there's really a simple answer: scientists believe that (at least on Earthlike planets) this basic form is the most conducive to intelligent life. Evolution only gives us what we need; anything we have that's extra (like that darn appendix) are remnants of something we used to need and have, and evolution has gradually reduced its role. The reason we don't have three arms is that having that third arm wouldn't have given our ancestors any significant edge in survival over their two-armed cousins.
So we've evolved to the bare minimum that's needed for our survival (given the current conditions). Two legs and bipedal motion for agility and mobility. Opposable thumbs, to manipulate tools. Two eyes, for binocular vision. Two ears, for directional audio sensing. Main sensory organs located close to the cerebrum for quicker response. Head mounted on top of the body to provide the highest possible point of view. On an M-class planet like ours, physical characteristics such as these would be the most conducive to the development of sapient life, and this development of human intelligence and culture has enabled us to adapt ourselves and our surroundings that we can survive in a wider range of conditions, so we are no longer limited by our physical characteristics.