As a whole, Star Trek - especially the Next Generation - posits a world in which humans were bastards, and rarely loses the opportunity to lecture their 20th-century viewers on how far we still have to go. Good news, though; we get better. In fact, we're even sorta charming, especially to advanced races who gauge others for 'potential'.
Even so, in one episode of Star Trek: Deep Space Nine, Quark the Ferengi lectures Commander Sisko about how his species never practiced slavery or genocide (particularly anvilicious as it's already established that Ferengi not only did keep slaves but still do (sort of) - anyone who goes into debt they can't repay is legally enslaved to their debtor. This also ignores the extreme sexism his race continues to practice). He also tells Nog in "The Siege of AR-558":
"Let me tell you something about Humans, nephew. They're a wonderful, friendly people - as long as their bellies are full and their holosuites are working. But take away their creature comforts... deprive them of food, sleep, sonic showers... put their lives in jeopardy over an extended period of time... and those same friendly, intelligent, wonderful people will become as nasty and violent as the most bloodthirsty Klingon. You don't believe me? Look at those faces, look at their eyes..."
The Vulcans are a more extreme example of former bastards. They often act condescending to other species, but the subtext is often that they realize that since they were bastards, other species can benefit from logic as well, and often get shirty when they don't. A young Tuvok from Voyager was once shown complaining about humanity always expecting other species to be like them, apparently not recognizing a classic Vulcan move when he sees one.
This is expanded upon in Star Trek: Enterprise. Vulcans are cold to humans, because they recognize so much of themselves in us. We went from a nuclear holocaust to warp travel in 100 years. It took the Vulcans 1500 years to do the same, and they learned to calm their violent nature through logic in the meantime. They see us as their unreformed society, but with the same technology, and it horrifies them how violent that means we could be.
The jabs at humans that Spock and other Vulcans like to make via examples from human history, however, go uncalled-out, even though all indications are that Vulcans were just as bad in their own early history. Spock himself admitted that Vulcan, like Earth, had its warring colonizing period that was considered brutal even by our standards, and that some Vulcans (you might know them as Romulans) still hold to their warlike roots.
Fraggle Rock stands dedicatedly on the "humans are misguided" side. Uncle Traveling Matt quickly dubs us "the Silly Creatures", which really says it all. On the few occasions Doc threatened the Five Races, he did so without realizing it (shutting down the pipes in his house shuts down the water supply for the Fraggles, Doozers, and Gorgs). When he finally meets Gobo face-to-face, he's careful to take this sort of thing into consideration.
Most behaviors that Traveling Matt observed in humans weren't silly at all — not even, in many cases, the way he misinterpreted them. For example, he thought paperboys fed hungry houses. The main exception is that when humans noticed him, they apparently mistook him for one of them.
Not really avoided in The Muppet Show or its movie spin-offs. As far as the biggest bastard Kermit ever met is concerned, Roger Ebert said it best: "As soon as Kermit gains legs, he meets a human with an unsavory use for them."
The famous anti-hunting rendition of "For What It's Worth" featured little woodland animals singing about "a man with a gun over there", and periodically ducking under cover as trigger-happy human hunters blundered through the scene, firing at everything that moved.
And then promptly subverted at the end when the hunters reveal they were trying to bag construction equipment.
Henson also wasn't above taking a stab at the trope:
Doctor Who, particularly the revival series, sways between Humans Are The Real Monsters, Humans Are Idiots, Humans Are Misguided But Well-Meaning, and even on occasion Humans Are Absolutely Frickin' Awesome, sometimes within the same episode. Which is probably as close to reality as you can get really, since humans generally show capacity for all of these things, depending on all kinds of factors.
Sarah Jane Smith: Because you have such good taste.
The Doctor: That's true. That's very true.
Remember the Ood from "The Impossible Planet" / "The Satan Pit"? We get treated to this trope in a later episode "Planet of the Ood". The humans who found them isolated the Ood Brain (the core of their hive mind) and after an indefinite amount of time started to hack off the Oods' hind-mind (the external chunk of brain sticking out of their face that govern personality) and replace them with translator orbs. Of course, not all humans are bastards: there are still people protesting against the slavery.
In The Christmas Invasion, after Harriet Jones has the retreating Sycorax ship blasted into smithereens, the Doctor is so angry that he briefly seems to lose all respect for humans in general: "I should have told them to run, as fast as they can, run and hide, because the monsters are coming: the human race!"
In the third season finale, the creatures that the Master uses to terrorize the planet, literally decimate the population, and enslave the human race turn out to be the human race from the future.
"The human race. Greatest monsters of them all."
Even more of a downer when you realize these are the same humans that the Doctor gave such a giddy "humans are indomitable" speech about in an earlier episode of the finale.
In "The Doctor's Daughter", humans are far more violent than the Hath.
A prime example in "Midnight"—no one knows that the Monster of the Week is, or what it can do. It's possessed a woman, and the humans trapped in with her start discussing what to do. If the Doctor weren't there to talk them down, they would have thrown her out of the train they were on. When it possesses the Doctor, they almost throw HIM out. All because they were scared.
In "The Beast Below", it's revealed that the engine for Starship UK is actually a Star Whale, the last of its kind. In order to keep the ship afloat, the whale is regularly tortured. The Queen chooses to forget this every 10 years, as she believes the alternative is to doom the entire population by releasing the whale from captivity.
Worse, each year every citizen would go into a room and find out the awful truth. They would then get a vote: Forget or Dissent. The first button caused the last few minutes to be erased from their memories, allowing them to live in blissful ignorance. The second button dropped them into the basement to be fed to the Star Whale. Children who fail in class are also treated to the latter, although the Star Whale doesn't want to eat them.
Amy overcomes this trait after first succumbing to it. Despite the seemingly impossible situation, she realizes the Star Whale's fondness of children is what led it to Earth in the first place, and if she frees it from prison, it will stay for the children's sake.
Doctor Who And The Silurians is practically made of this trope. Despite all the Doctor's best efforts the humans' greed, stubbornness and fear sends the situation spiralling out of control, culminating in the Brigadier murdering an entire race of hibernating people. While the Silurians wanted to destroy the humans at least as much, they do show nobler tendencies, as the Old Silurian is the only morally respectable character aside from the Doctor and Liz and even the young Silurian's choice to sacrifice himself for the good of his people contrasts with the petty, selfish and emotional reactions of the human characters.
In fact, pretty much every appearance by the Silurians throughout the series will at least invoke this trope once or twice.
Some stories of the First Doctor feature this trope. In "The Sensorites", the Sensorites fear humans because a previous expedition of humans that came to the Sensesphere have been poisoning the water supply.
In "The Rescue", the villain of the piece is a man who killed the survivors of his spaceship crash, as well as the local alien population. He has been posing as one of those aliens to keep the only other survivor, Vicki, in check. He does all this because he killed a man on the spaceship, but it had not yet been reported to Earth before the crash, prompting him to kill all the witnesses and use Vicki to corroborate his own story.
The Doctor Who spinoff Torchwood uses this trope too. Perhaps the most disturbing example is the episode Countrycide, which is notable as the only episode in the Whoniverse not to contain any science fiction elements (other than Jack's immortality and a few pieces of Torchwood technology, both of which are incidental to the plot). The villains are human cannibals who engage in horrifying acts purely For the Evulz. However, it is brought out on a truly large scale in Torchwood: Children of Earth and Torchwood: Miracle Day, where the primary antagonists that the Torchwood team must deal with are really evil humans, with the alien threat being more of a catalyst than a core issue.
Battlestar Galactica: While the Cylons definitely hold that view towards humanity, at least in the first couple of seasons, Cylons are pretty much better than humanity at everything. Including self-righteous hypocrisy (given they make statements like "humans don't respect life like we do" after exterminating most of humanity in a nuclear holocaust and about to gun someone down).
Supernatural: While Sam and Dean usually fight supernatural monsters, the first season episode "The Benders" involves humans who hunt down other humans for fun, the second season episode "Houses of the Holy" involves a man with dead bodies in his basement, an email-using pedophile, and an attempted rapist, all of whom deserved their instant death, and the third season episode "Sin City" features a demon talking to Dean about how much humans suck. The fourth season episode "Family Remains" involves a man who raped his daughter and then shut the resulting twins away under the house, where they became animalistic scavengers. "The Benders", "Family Remains" and "Thin Man" are notable for being the only episodes so far that don't actually involve anything supernatural, just urban legend-like events of a mundane sort. Dean: "Demons I get, people are crazy."
Interestingly, Lucifer believed that Humans Are The Real Monsters and was furious that God showed more attention to those "murderous hairless apes" than to someone who was perfect and wonderful, like him.
LOST seems to be going this route with the overriding conflict between Jacob and the Man in Black/Smoke Monster:
MIB: They come, they fight, they destroy, they corrupt. It always ends the same.
Jacob: It only ends once. Everything that happens before that...is just progress.
Subverted in an episode of the 80's The Twilight Zone revival, when aliens arrive on Earth and announce that they seeded the planet with humans ages ago, but now they are destroying us because they were attempting to breed warriors, and we aren't big enough bastards.
The original Twilight Zone is rife with this trope. In The Monsters Are Due On Maple Street as well as in The Shelter a suburban town tears itself apart after a perceived invasion/attack. The Eye Of The Beholder and Number 12 Looks Just Like You highlight our superficial views on aesthetics (True Beauty Is on the Inside). Third From The Sun (with a hint of Nuclear Weapons Taboo) and Probe 7, Over and Out show our repetitive barbarous irresponsibility. I Shot An Arrow In The Air shows our hatred and evil tendencies in the face of death. The Rip Van Winkle Caper shows how greedy we can be even with our "friends". The Little People shows Drunk with Power, and perhaps the best example of this trope; People Are Alike All Over where alien benefactors who shower gifts upon an earthling reveal their demeanor as a ruse when they abduct him for exhibition in a martian zoo (Face-Heel Turn)
Rod Serling's other series Night Gallery had an episode where a professor is teaching the students to hurt one another. The class are robots. There was a global war and the world needs to be repopulated. The robots aren't being taught to be assholes, they were being taught to be human.
Shown a couple times in Farscape, especially in the episode "A Human Reaction" where John returns to Earth and the government immediately imprisons and kills both D'argo and Rygel to study alien anatomy. The entire episode paints a particularly bleak picture of the human race. Possibly subverted in that it is actually all an engineered environment made by aliens that are using John's memories and knowledge of the human race to judge how humans will react to aliens. Apparently John doesn't have too much faith in humanity.
Somewhat justified in the season 4 episodes dealing with several of the humans' reactions and the crew's interactions when they actually do reach Earth.
Subverted/inverts another trope at the same time. Sebacians aren't Scary Dogmatic Aliens. They're genetically engineered humans.
In an episode of Smallville, Brainiac claims that humans are worthless and trying to save them is a waste of time. To prove it, he causes a blackout (one that affected airplanes in flight), and everyone except for the main characters goes completely nuts: rioting, looting, sending a car through a building. Clark Kent exhausts himself running around the city trying to keep the peace, until his friend Chloe tells him to just find Brainiac and defeat him.
Clark starts thinking this when Davis Bloom proves that he is pure evil after he had been cured of his Hulk-like transformations into Doomsday.
Byron from season 5 of Babylon 5 is convinced Mundanes Are Bastards, that when telepaths engage in actions such as murder and Mind Rape, it's only because mundanes have pushed them to it. However, this is obviously not the case, as he and his people end up doing plenty of horrible things out of a sense of entitlement, and Byron's statements probably made things worse with ideas of "we deserve this" and "it's their fault, not mine".
When humans dig up a Shadow Battle Crab on Mars, they look at its horrible blackness that induces internal screaming, and immediately think "Hmm...how can we make this work for us?"
To be fair, Shadows are even more misguided then humans, but are not inherently evil (though they may look it). Humans on the other hand just have an affinity for power, even if it wasn't earned.
In episode 5 Kali decides that the human race needs to be wiped out after her date is shot in a pigeon culling. Her plan involves breeding a master race of "pigeox" and when it turns out to be a normal pigeon with red feathers she tells Vince to eat it.
In Andromeda, the character Seamus Harper is a human who grew up on Earth. Earth in this 'verse has been invaded by both the Horde of Alien Locusts Magog and the genetically-engineered Nietzscheans. As Harper tells his alien shipmate Trance Gemini in one episode, the Nietzscheans were worse because they were human. Granted, not that they just were capable of even more oppressive, creative cruelty than the brutal monstrosity of the Magog, but that the fact that, despite their superior attitude and holding themselves apart like a different race entirely, they are not another species and that makes it worse.
In another episode, Harper wonders aloud if Castalians (a genetically-engineered human variant that breathe water) eat fish or if it would be like humans eating monkeys, and Captain Dylan Hunt points out that humans have eaten monkeys, and other humans.
HG Wells in Warehouse 13 comes to this conclusion after her eight-year-old daughter was murdered.
'"Open your eyes, Myka! Have you seen the world in which you live? The divide between rich and poor! Hunger and famine! War and violence and hatred all flourishing beyond control! Indeed, men have found new ways to kill each other that were inconceivable in my day, even by fiction writers!"
In Once Upon a Time, Giants see humans like this. They turned out to be right, because Two humans fool the one giant that believed that humans are not only violent, ambitious creatures into giving a way the location of the beanstalk and thus allowing them to wipe most of the giants for treasure and beans.
Peter Watts subverts this in "Bulk Food", a short story where we finally make the technological breakthrough that allows us to communicate to whales. As it turns out, whales are just as awful as we are, and orca Matriarchs are more than happy to sell off some their stragglers as food and entertainment.
Well, no one expected the whales to be such assholes.