Alien Physiology

What will an alien look like? If you follow the viewpoint of most television sci-fi then all aliens will be men in rubber alien suits. The producers of Star Trek seem to think aliens are just like humans with little latex ridges on the noses or foreheads.
The reason for this anthropomorphism on TV is that it's cheap. The alien in the Movie Alien was gross and ugly and we surly would never be able to discuss our new age feelings with such a creature. It cost the movie producers much more than a little latex on the bridge of an actors nose.
The truth is that we are much more likely to meet Sigourney Weavers's alien than a Bajorran.

What kind of aliens will we meet in out wanderings in space? Will they be like us?
This can be answered in part by asking what kinds of animals have evolved intelligence here on earth?
The ratio of brain to body weight is a generalized way of looking at intelligence. It makes sense that a large brain will mean a higher intelligence. A large body needs a larger brain to control it so you have to allow that an elephant's brain has more housekeeping to do than actual higher thought and might not be as smart as his large brain indicates.
Animals with the biggest brains are Whales, Elephants, Porpoises, Man, Chimpanzees, Baboons and Wolves. If you normalize the body weight, the order of size is Man, Baboon, Monkeys, Camels, Porpoises, Kangaroos and house cats. (I knew my cat was smart).
If you rank animals by human type intelligence tests, the large water mammals fall off the list and Horses, Pigs, Dogs, Ravens and Parrots move up the list. (Cats don't sit still for tests.)
Some creatures have incredible memories. Surprising, the octopus has a large brain and in tests shows the ability to memorize things like the shapes and sizes of objects or the scent of another octopus. Octopus owners are amazed by the responsiveness of octopus.
Group creatures like swarms, flocks, schools and herds seem to have emergent properties which reflect communicated information that cause the group as a whole to display behavior which is smarter than any individual.
So what is the standard for earthly intelligence? Two legs don't seem to be a requirement. Most smart animals walk on four legs. Birds and primates can walk upright. Birds do it because they have wings instead of arms. Man walks upright because he needs to carry things in his hands. Kangaroos hop upright because they are very strange creatures. Horses, pigs, wolves, dogs, camels and elephants walk on four legs because they need to be stable or need speed to survive.
The truth is that there is no body shape that easily connects to intelligence. On earth, multiple legs from 4 to 1000 was the standard until vertebrates started walking in the mud. After that, the four leg rule seems to have been cast in stone. We all descended from the first amphibious ancestors that learned to walk and inherited the 4 leg rule from them. This could have been six legs like insects or eight legs like spiders, or multiple legs like centipedes, but we started out with four legs and all our ancestors stuck with it. But insects and other polypod creatures are very successful. The two legged creatures are really four leggers with two of the legs adapted to other use.

Aliens will have just about any body configuration that we can conceive of if the earth is any guide. But what about physical attributes like eyes and noses and mouths and hands and thumbs?

An intelligent species will probably be able to manipulate the world with appendages. An intelligent species that can't make tools won't get to the stars. The hand is a good all purpose manipulator as is the octopus's tentacles and the elephant's trunk. Humans who loose the use of their hands get along fairly well with toes or lips. Who can forget the scene in the move “Freaks” where the armless and legless man rolls a cigarette and lights it using only his mouth? We can expect aliens to have hands or claws or tentacles or a trunk or a snaky body so that they can grasp things and make tools.
Will an alien have two eyes? Symmetry seems to be a standard of life on earth. Of all creatures that make our intelligence lists, only the octopus doesn't display binary symmetry. He is symmetric, but has no obvious left and right sides. Octopus experts will probably correct me on this.
Binary symmetry - having a left and right side seems to be the right amount of redundancy. Lose the left hand and you still have a right hand. Loose the left eye and you still have the right eye. Two eyes also give us binary depth perception. More than two eyes would not be especially beneficial. Two hands let us grasp with one and manipulate with the other. Three hands would get in the way. The examples in nature that we have of more than 2 eyes are for creatures that have very simple eyes and need multiple receptors in order to make out changes in dark and light or nearby motion. Two seems like a probable number for most things like hands, ears, testes and nostrils.

Will aliens ever look like us? The answer is Probably not but there is a theory that there are only a few basic body types possible. The example that is always given is Dolphin, Shark and Ichthyosaurus. These are three animals with the same body types which are totally different kinds of creatures. One is a fish, the other a mammal and the last is a reptile. They look so much alike that a layman would not be able to tell them apart without years of watching the discovery channel under his belt.
Could it be that man is a basic type and that there would be a tendency for evolution to create intelligent beings with two arms and two legs and a head? Bipeds are rare on earth. Man walks upright because he probably had the need for speed while bringing food home to the family. He would pick up food in his arms and sprint on his hind legs to get home. A woman could pick up her infant child and run fast enough to save the both of them. This would also allow him to eventually use tools and would help in the development of useful hands. Thumbs would help him to climb trees and coincidentally to pick up large bones for use as clubs. Creatures that lived on plains on the edge of forests that previously lived in trees might develop as humans did.
It is much more likely that four legged animals with trunk like manipulators or extended lips or mouth parts would be the tool makers on any planet. Evolution wouldn't make two legged creatures form scratch and they'd have to evolve from four leggers. It's hard to think of that many scenarios where the four leggers would gain anything by going upright on two legs. The birds did it because they needed their wings. The Kangaroos did it for some unknown reason - but probably, like man, they needed speed while holding their young or food. It's not impossible that we'll meet bipeds, but not real likely.

How will aliens solve the problem of sex? Sex is a requirement for fast evolution. Traits are passed down from parent to child, but when there are two parents, the child can inherit from both of them. This spreads mutations around in a species far faster than can be done without sexual reproduction. It seems two sexes are sufficient and more would be redundant. Sex is a real requirement for the evolution of alien life. Whether there will be male-female type differentiation or another solution is up to your imagination.

One thing that I know will be different is alien sexuality. Humans have lips and breasts because they are mammals. The lips are used for sucking and the breasts are used to provide milk. This is a rather specific solution to the general problem of feeding young. The obvious solutions are for the parent to pre-chew food or even partially digest food and regurgitate it. Birds do this. Bees have complicate variations on this. The breast solution seems a little strange (although I personally like it).
Very few aliens will have breasts and lips and of those that do, the breasts might be located in armpits or in pouches on the stomach and they will not need large alien bras.
The male and female genitalia seem to be hard to explain away as being the obvious solution. All that is needed is a good way to get germinating material from here to there. On earth there are lots of complicated ways to do this. Pollen and bees springs to mind. Fish lay external eggs which are fertilized externally. There is often some kind of tool for placing sperm and some kind of receiving place for taking it in, but these are in no way similar to the human solution. The placement of our reproductive organs was set in stone for us millions of years ago and proved successful enough that there was little variation afterwards. An alien may have evolved differently and accidents of evolution could have placed the sexual organs at many interesting places.
Even if an alien walks erect and superficially looks like a humanoid, it will be very unlikely that your characters could have sex with such a creature.

The only time that you should humanoid characters in your science fiction stories is if they are for TV or the movies. Sci-Fi (as opposed to SF which is the literature of Science Fiction) deals with unsophisticated audiences. The story line is usually a western or a war story with space or alien elements. The time it takes to develop explanations about alternative aliens is not available in the short format so it's either evil beast-like alien or man-in-a-rubber-suit aliens. Sci-Fi likes female aliens with big breasts -- by far the least likely alien we will ever meet - but at least it provides the men in the audience with something to watch when the space ships aren't shooting at each other.