(Or: a discussion of science fiction clichés)
Long ago, I created a space opera universe, with high hopes of setting all kinds of awesome stories in it. That didn't work out. Took me years to write just one. Even writing down all I knew about the setting didn't help. After some reworking, it finally yielded another story written by a friend, and a forum-based roleplaying adventure. And that was all.
My third attempt at worldbuilding came much later, and went straight to science-fantasy. But even though almost everything changed, most of my old principles turned out to have aged just fine. So here they (still) are. Enjoy.
Earth should not be special in any way
Aren't you annoyed by the anthropocentrism and Terracentrism of most science fiction? I mean, when Earth isn't the pinnacle of galactic civilization (usually without justification), it must be a long-lost world of legend. Egregious offenders include Star Trek in the first category and the Foundation in the second.
What is so special about Earth? That we happen to live on it now? An alien couldn't care less about that. In a galaxy with many advanced civilizations, we'd have to work hard to even get noticed. Grow up, people! Nobody's special.
For an example of this aspect done right, check out the webcomic Terra.
Why only a handful of important planets?
For that matter, isn't it funny how in most science-fiction we are told there are hundreds or thousands of major worlds, but only a handful of them seem to matter at all? Like when a multi-thousand world galactic empire has a defense line relying on three (!) planets, namely in A. E. Van Vogt's 1959 novel War Against the Rull. Well, think of it this way: according to Wikipedia, there are no less than 27 cities with over 5 million people on Earth, for only about 200 countries. That's a pretty large ratio. And speaking of countries, I'll bet that all but the smallest have more than three military bases...
Of course, a single planet already provides enough room for countless adventures -- there's simply no need for most space opera stories to even go into space at all! But if you do, at least take care not to sound ridiculous.
Aliens should be well fleshed out
While bumpy foreheads are entirely justified (see below), the uniformity of the typical sci-fi aliens is downright offensive. What, they don't have different races on their planet? No different countries, languages, customs, nothing? They're all carbon copies of each other? That's a hideously simplistic proposition. I'm not saying every fictional alien species should be as complex as our own (it would be a tremendous amount of work), but you can at least make up two or three variations of each.
Example: the fantasy world of Forgotten Realms, which is otherwise quite clichéd, features several varieties of elves, dwarves, giants, dragons and so on. Just enough to make you feel there's an actual history behind each of those races.
Aliens should be truly different
I used to think quasi-human "aliens" with bumpy foreheads were the bane of science fiction, but that was naive. You don't even need the excuse of TV budgets: just remember that sci-fi is not about future tech and distant worlds, but about ourselves, right here and now -- a distorted mirror.
That said, when each and every alien is basically just a caricature of some human stereotype, and we get to teach them right from wrong -- because, isn't it, our norms are somehow universally the best -- the story just becomes insulting. The whole point of putting aliens in a sci-fi story is to give the audience a good look at themselves from a novel angle. Are our ways really the only possible ones, let alone the best? Think, dear writer! Use that creativity of yours!
Now, if you're so worried about explaining all those quasi-human aliens (like Star Trek: The Next Generation did in a ridiculous three-part episode), make our species co-exist in the galaxy with our transhuman and even posthuman descendants, like the Festival in Singularity Sky (Charles Stross, 2003).
Not everyone should have the same tech
Looking at our civilization as it is now, it's pretty easy to see that technology tends to grow uniform. The law of diminishing returns settles in, and sooner or later everyone converges on the optimal solutions.
What many science fiction writers have not noticed is that we are one sapient species on only one planet with relatively uniform conditions. What is optimal for us will be unlikely to be optimal for an alien civilization as well. Especially as they may know things we don't, and vice-versa. The universe is weirder than we think; why make it bland?
Even if you don't really have aliens, like in my newer setting, you can still have a faction living on a Stanford Torus, while another has reactionless drive and energy shields, with yet a third relying on magic. Yes, that's science fantasy. So what?
Acknowledge the vastness of space
It's one thing to compress the action -- again, for the benefit of the audience -- but both filmmakers and writers are overdoing it. Starships engaging in battles at shorter ranges than even real life vessels, maneuvers never taking more than a few seconds (fighter planes in space? again?), interstellar travel times omitted completely (and never mentioned to boot, presumably to avoid inconsistencies), such tactics remove any sense of scale. The characters may just as well be kids playing in their backyard. And then, why bother setting the story, you know, in space?
Know what rules you're breaking
Everyone knows space is silent and laser beams move at lightspeed, while spaceships can never exceed it. Everyone knows, but nobody cares, because telling a good story is more important.
Not enough people seem to understand conservation of energy, or conservation of momentum, and those are the very pillars of physics. Or that Earth's magnetic field can only protect us from cosmic radiation because it's much bigger than the planet itself. Or that we actually tried to build arcologies, and failed shamefully, even on a small scale.
Never mind that ignoring such things perpetuates the myth that we can somehow move to another planet after we destroy the Earth; but people can tell when you're breaking these rules on purpose, and when you don't even have a clue. And they'll rightfully mock you for it, so get a clue.
Stop worrying about faster-than-light travel in, you know, science fiction. It's physically impossible, so what? Building a Bussard ramjet is so difficult it might as well be impossible; that the laws of physics technically allow one to exist doesn't make it plausible. Might as well assume quasi-magical FTL and worry about telling a good story.
Also, let me stress the point about quasi-human aliens: they are an essential plot device. Just remember that even on Earth, among plain old humans, we have cultures strange enough to qualify as alien. Imagine the divergence after a few thousand years of people living on different planets, with varying local conditions.
For more information, check out the Big List of Overused Science Fiction Clichés (available on several websites). And remember that clichés are not the same thing as tropes, even though sometimes it's hard to draw a line.