Similar to the swords in modern fantasy complaint, how about the aliens who are somehow defeated when they attack Earth. Humans have the ability to destroy all life on Earth. How could aliens master interstellar travel and yet fail to bring along some nukes?
because conquering something is a lot harder than just destroying it.
(insert obligatory War in Iraq comment here.)
I don't know, man. If the aliens can cross interstellar distances, and are planning on conquering Earth, their technology would be so far ahead that we would have a hard time mounting an insurgency. I think a more apt analogy would be European colonialism and the indigenous people of North and South America and Australia.
What I'm thinking about here are the beam weapons that aliens seem so fond of. In Independence Day the aliens terrorize humans by zapping the Empire State Building, and in War of the Worlds they have that heat ray. Why not just nuke...not even nuke, drop an asteroid on every major city. That would get our attention.
Please don't confuse Independence Day with Science Fiction. 
If their technology was that far ahead, they would probably already know we are here, and have already found a way to have beaten us before they got here. The European colonial analogy is a pretty good one, but even assuming the Europeans had a 2000 year technological advantage (and there are people on these boards who could answer establish that number much better than I could), that probably doesn't come to close to what the aliens would have. Isn't the universe 13 billion years old? Given that amount of time, a space faring civilization would probably have a technological advantage of several million or even hundreds of millions of years. Sure, they would have obstacles to overcome that the Europeans didn't have (like brining food and atmosphere), but they would have a long time to have figured that one out. In order for something like "War of the Worlds" or "Independence Day" or "Signs" to happen, you would have to a civilization that was just far enough ahead of us technologically, just close enough to get here, just war like enough to want to attack us, and either just desperate enough or just stupid enough to commit that many resources to the job without a full proof plan. There are so many coincidences that would have to come together that the odds of it happening are pretty much nil.
That doesn't stop it from being the basis for some great stories, though. 
Another possibility that I just thought of is this: Perhaps there is some factor that we currently don't know about that defines some kind of upper limit to intelligence, regardless of what organism develops that intelligence, i.e. the most in intelligent that a mammal or an insect or a worm could ever become is all fixed at the same level. I could see a species reaching that point, inventing everything it is ever going to invent and then just treading water, technologically. If that level allows for interstellar travel and if these different species evolve far enough apart, I could see a situation where lots of different races, all on equal footing, would be competing for the available resources of the universe - interstellar war.
Clint, others, have you guys ever read William Barton's "When Heaven Fell"? If not, based on this conversation, you may REALLY enjoy it if you can find a copy. Here's a quick teaser -
The world -
Earth was invaded by the Spahi Mercenaries under employ of "The Master Race". They subdue the Earthlings in a few weeks. 5+ Billions humans are killed. The remainder live among the ruins. A very select few can test for a position in the Spahi Mercenaries. Athol Morrison is one of the select few who passes the entrance exam (effectively a survival test) and goes off to do the bidding of the overlords.
The actual invasion is only talked about in past tense, though Athol was old enough to remember when it actually happened. He is in his mid 20's when we meet him (coming home on leave), he was a little kid when the Spahi invaded. The only world he's really ever known is the devestated mess that is post-invasion Earth.
The bulk of the novel is about his three week leave, reconnecting with his family and friends among the rubble and destruction of his home town. He's an outsider now because he is a soldier of the enemy army. The peripheral bits of the novel are about how the Master Race has expanded and absorbed so much of the galaxy that they are starting to butt up against the borders of another super-powerful race and they may be overrun.
Athol learns that resistance movements are occuring not only on Earth, but even on the home planet of the Shrahh, a race that resembles Tyranosaurs who are the largest and strongest soldiers in the Spahi.
Athol Morrison -
He's big and broad shouldered, in his mid 20's, and has no regrets about the military organization to which he belongs because it's better than eating food cooked over garbage fires and doing forced labor among the subjugated Earth.
The Master Race -
A superintelligent race of self-replicating little black boxes that were created by a race of small furry creatures who have reverted to an almost pet-like mentality and intelligence - they are sort of like hamsters when we meet them.
The War -
Earth had just put her first FTL ship into Earth Orbit when the picket force of Spahi arrived to stake claim to Earth's resources. The captain of the Earth ship kamikaze'd the picket force and destroyed them. It took 50 years for the full might of the Spahi to return to Earth. Fifty years gave humanity time to turn ALL of their industrial production over to military development to try and fight off the incoming invaders.
The war lasted just three or four weeks. 125,000 Spahi were killed, 5+ billion humans were killed. Estimates in the book suggest only a few tens of millions of humans survived globally.
It's a really good and compelling, if depressing, read.