Mark "The Mangler" Wheeler#1 Contender for the heavyweight title.
I usually start from the single-cell concept and evolve the creature in my head. I want to create original creatures, but logical, scientifically sound creatures. And I'm not of the school that thinks everything is going to evolve into a bipedal humanoid. People who come up with those kind of "aliens" aren't even capable of looking around the planet and seeing the amazing diversity of form we have. So the aliens usually have a few things in common:
1) There are no "super predator" sentient beings: It's humanity's weaknesses that drove the evolution of intelligenge as an evolutionary advantage. If we had big teeth, big claws, armored skin, et cetera, why would we need to evolve intelligence? It's our vulnerabilities and weaknesses that drove developments like weapons, clothing, tools, etc. So the aliens may have unique physical characteristics, but the sentient ones all have ample weaknesses and no "super powers."
2) They do not look like people with crap on their face. I loath the "Star Trek" aliens. I know most of that is due to budget, which is cool for TV, but in books, the aliens don't have to look like people. I mean, come on, people, open a fucking science book from time to time.
3) They do not look like "wolf men" or "lizard men." The idiotic concept that out there, somewhere, another planet also evolved dinosaurs, but they didn't have the extinction event so the dinosaurs (or insert other animal here) grew to sentience is retarded. The odds of another planet producing a "reptilian race" similar to Earth reptiles is astronimical. Aliens evolve their own base structure from which species branch out. I make that base structure something unique, and make it something other than your standard bipedal quadraped.
4) Hatred is an evolutionary advantage: the concept that someday we will have this magical society where everyone gets along is a crock - that's the land of happy ponies, it doesn't exist, it will never exist. If we hate each other so much, and we all basically look the same, imagine how we'll feel about something that looks more like a nasty cricket than a person ... and, most importantly, imagine how they will feel about us. Racial tension, or species tension, really helps to establish the aliens as "real" to us, because that's something we see on a daily basis (if not in person, in the news, movies, history books, etc).
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"A common mistake people make when trying to design something completely foolproof is to underestimate the ingenuity of complete fools."