The player actually can bully a dragon in Zork II. Although truthfully, it's not so much "bully" as "disturb its nap, then annoy it with your puny sword until it incinerates or eats you."
In The Witcher, the eponymous Witchers have to take a lot of verbal abuse from normal people. None of them stops to ponder whether it's smart to mock someone who you'll need when you're once again troubled by some undead menace (a common occurrence in this world), and who can break the finest human fighters in half with his superhuman mutant reflexes and Healing Factor.
Phantom Brave: The People of Ivoire think main character Marona is "The Possessed One" who can kill them all by summoning armies of the undead. So they hire her to solve their problems, insult her, then cheat her out of payment. They do get better.
Goes double for anybody stupid enough to intentionally piss off Shadow.
City of Heroes: The thoughts running through every single street gangsters' alleged mind must be: "I live in a city where people wielding earth-shattering powers run around dressed in bright colored spandex. I'm bored and I have a baseball bat. Let's attack the very next person we see dressed like that!" The only question is whether it's dumber when they're attacking any hero they see or when they're entirely ignoring REALLY powerful heroes bearing down on them as if they weren't even there.
The second one is very clearly a useful survival strategy. Most of the time, heroes of a high enough level to mop the floor with a spawn of villains won't get enough XP from it for them to bother, but if the villains went around hitting first...
After a few days of lockdown in Devil Survivor, mobsters start to hunt down devil tamers. This either ends with killing a tamer who was trying to save them or a pissed tamer countering with summon demons.
The beginning of Overlord II has kids tossing snowballs and taunting the Witch-boy, a Creepy Child who blasts lightning with his hands and gains controls of vicious little Minions early on. It Gets Worse later on when after being tossed out of Nordberg by the village for The Empire, frozen in a block of ice, and later raised by an Evil Chancellor, he returns as a full-fledged Evil Overlord ready to either enslave or slaughter Nordberg.
Ar tonelico has an evil company of mercenaries that actively abuse and denigrate their magic-wielding partners. This is doubly stupid, since there's the obvious "oops I fireballed your face" factor plus being mean to them severely limits the power of the abilities they can use to help you.
Sure enough, at least one boss is defeated when he asks his abused partner to attack you, after literally enslaving her. She smiles, says 'No'...and uses her charged special on HIM.
This trope also turns out to be one of the major reasons for all the problems in the game and the reason the Big Bad is the Big Bad. Poor Mir.
In Yggdra Union, Gulcasa was born the first pureblooded descendant of the dragon Brongaa in hundreds of years. This made him a savior to his people, and gave him the right to the throne. The previous Emperor did not like this, and under his orders, Gulcasa was treated as a harbinger of disaster and abused throughout his childhood. Too bad for the Emperor of that time that Gulcasa is literally the descendant of a demonic dragon. At least the coup d'etat was over really fast. There was much rejoicing.
Done in Arc The Lad: when they find a more-or-less 5 years old child who's already able to kill soldiers by summoning flames, Seiyras scientists decide to turn him into a guinea pig: the adult version of said kid, last survivor of a genocide, tortured during his childhood, eventually teams up with the world's most wanted terrorist and is instrumental in destroying the Ancient Conspiracy for which the scientists worked.
Two of the Masters in Fate/stay night have a real problem with this. The first is Shinji, who only evades being killed because it would upset Sakura, Rider's real master. The second is not so lucky and is in fact dead quite a while before the story starts. Caster's Master was jealous of how much better a magus she was, so he put a power limiter on her and then abused her. She got tired of it and tricked him into using up his Command Seals, then brutally murdered him.
If you choose the "Earthborn" origin in Mass Effect (you were born on Earth, orphaned, and grew up on the streets), you eventually run into a former member of a gang you used to be a member of. Commander Shepard is both the commanding officer of a Systems Alliance black ops ship, and a Spectre, essentially given carte blanche by the Citadel Council to do whatever they want. Your "friend" tries to blackmail you, because apparently he thinks revealing that you were a former gang member would ruin you; even though the Alliance and Council are willing to look the other way if you mow down mind controlled civilians or exterminate an entire race. You can choose to point out that you're legally authorized to execute him where he stands... or you can just shoot him.
Really, regular mercs inexplicably trying to kill Shepard at every possible moment fits this trope, regardless of the origin. Harkin, a corrupt cop from 1 and 2, even taunts Shepard by asking if they think they can get him. There are also several small encounters where someone tries this on Shepard, who can sometimes point out either that a) They are Commander Shepard, aka the galaxy's biggest badass and just what the hell do they think they are trying, or b) They may not know they are dealing with Shepard (or may not believe it), but they can surely see how badass Shepard is, so shut the hell up.
Quite possibly the best example of this in the series is Warden Kuril, who attempts to knowingly imprison Shepard, the most Badass person in the galaxy, and hold him/her for ransom or sell him/her on the black market as a slave. It doesn't end well for him. Especially stupid, since you belligerently refuse to surrender your weapons on entering the prison, even threatening Kurill, and he (still fully intent on capturing you, remember) lets you keep your weapons. Even more stupid if you're playing a class that wouldn't have been significantly less dangerous without weapons. What exactly was his plan for imprisoning a Shepard that could throw him across the room with a mean look?
In the Mass Effect: Redemption comic, some shuttle pilots try to get additional "docking fees" from Liara T'Soni. Liara, as it turns out, is a powerful asari biotic who works with Commander Shepard. Even if she didn't, all asari are biotics to varying degrees of strength. And they don't even need implants to use their powers. Those pilots should've known better.
To the mad scientists and corrupt corporate executives of the galaxy: if a group of heavily armed people led by a Spectre comes up and tries to arrest you, pulling a weapon is not exactly the brightest idea. This happens three times in the first game alone.
During Grunt's loyalty mission in the second game, Gatatog Uvenk decides to pick a fight with Grunt, Shepard, and their squadmate... immediately after they have survived a fight on foot with a thresher maw (a hundred-foot-tall monster that spits acid and crush buildings with a swipe of a tentacle). Especially stupid if, rather than simply surviving the fight, Shepard and co. actually kill the maw outright.
To be fair to Uvenk, he wanted Grunt in his clan, because he's the badass that survived/killed a thresher maw on foot (Human battlemaster +1 notwithstanding). It's just that his sales pitch was so poor that a fight was inevitable.
In Tales of Rebirth, Hilda, a "Half" (Half-Huma[n] half-Gajuma), was always despised when she was a kid (and still is). Which wouldn't make much difference, except that Halfs, despite having a weaker body, have much stronger and harder-to-control magic than both Humas and Gajumas. (Un)fortunately, she never fought back.
A literal example in Breath of Fire IV. The Empire keeps messing with both Ryu and Fou-Lu even though they are quite aware of what they are. Needless to say, neither ends well.
"And people actually voluntarily attack you? Are they just stupid?" - remark of Sergeant Kylon to the Warden in Dragon Age: Origins after a side quest.
Also lampshaded when you first meet Flemeth during your initiation into the Grey Wardens. One of the Mauve Shirts in your party accuses Flemeth of being a witch, and the other one says "If she is a witch, do you want to make her mad?"
Flemeth in regards to this trope is doubly amusing when you find out she often turns into a dragon.
There's also a rather sad example in Lothering, where a band of refugees attack you out of desperation to collect the bounty Loghain has placed on your head.
If you tell a couple of bandits that you are the Warden Commander in Awakening, some of them immediately realise that it's better to leave, while one actually jumps off of a cliff and likely to their death, just to avoid having to fight you.
Arl Howe is probably the king of this trope, as well as Do Not Taunt Cthulhu. If you took the Human Noble origin, he brags to you about how he butchered your family.
Chantry zealots such as Petrice go out of their way to escalate hostilities against the hundreds of elite Qunari warriors who were shipwrecked in Kirkwall. The Qunari have done nothing against Kirkwall for years despite the Arishok's growing disgust with the Wretched Hive of a city, since they are busy looking for their sacred relic. They aren't even actively looking for converts to the Qun — people are joining them of their own free will. Near the end of Act II, when Petrice murders Seamus Dumas after he joined the Qun, the Arishok warns Hawke that the provocations the Qunari suffered have finally worked and later launches a full invasion of the city.
Likewise, we routinely see Templars or Slavers threatening mages who don't have good control over their powers (or cause them to become desperate enough), that the only way out they see is to allow demons to possess them and become Abominations.
Despite being well known as the Champion of Kirkwall by Act III, the amount of people who try to murder the person who defeated the Arishokin single-combat is particularly baffling, especially if Hawke is a Mage.
Several post-non-scripted-battle quips from your comrades fairly well lampshade this, usually different iterations of "When will they learn? Messing with us is suicide."
When she was five years old, Alma Wade was found to have extraordinary psychic abilities, and they were growing more powerful. So her father had her put in a lab where she could be studied and others protected from her. However, he and others involved in the project decided to step it up by sealing her away forever and inducing a permanent coma, because she was proving dangerous to them. Then they artificially impregnated the now-teenage girl, twice, in an effort to make viable telesthetic offspring that could be used for their company's purposes. She woke up during both births, and screamed to let them keep her babies. Then they deem her still too dangerous, despite the coma, and shut off life support and leave her there forever. She doesn't die. And when Alma escapes years later, she is apocalyptically pissed off, and oceans of blood follow. The people involved in the project get the worst of it, including her father.
This happens a lot in Oblivion (and Fallout 3, for that matter). You can be walking around carrying a glass warhammer the size of a wolf, clad in the finest armour in the land custom made for you by the Elder Council, be hailed in the street as the Champion of Cyrodiil, the Grand Champion of the Arena, be known as the leader of the Fighters and Mages guild... and some punk will jump you by himself and demand that you give him a paltry sum of money or he'll kill you. Similar things happen in Fallout 3, where you can be a walking tank packing a plasma rifle and someone will try to take you down with a bat. This is particularly unforgivable, as the local radio announcer is constantly updating the entire wasteland with information on how badass you are.
This trope can also be applied to you. When LibertyPrime is repaired and attacking the Enclave, you "can" attack him, though doing so is a surefire way to get killed because he NEVER dies no matter what you shoot him with and he can kill you in one hit with his Eye Beams. In other words, DON'T DO IT.
Ironically, this happens to Liberty Prime itself in Broken Steel. After continually pushing on the Enclave after the assault on the purifier in Fallout 3, the Enclave pushes back. Hard.
One Apocalyptic Log you can find in The Pitt expansion for Fallout 3 is the journal entry of a steelyard manager describing how his workers rioted due to being forced to leave after being replaced by new mechanical workers. Robots based on the Securitron pattern. When the robots showed up, the rioting humans tried to attack the heavily armored, laser-blaster-wielding, steel-claw-equipped, notoriously violent and unstable robots. The result is... too horrific to mention.
In Fallout: New Vegas, if you have bad standing with Caesar's Legion, you will attract assassin squads. Said four-man squad (who admittedly tend to be well-equipped for the task) will run up to you and proclaim that Caesar has ordained your death for your crimes against the Legion, before attacking. Said crimes can include killing Vulpes Inculta, singlehandedly wiping out Cottonwood Cove, Nelson, or the Fort, not to mention killing the previous assassin squads.
In a very amusing example, if you're a female Courier, a low ranked Legion soldier armed with nothing more than a knife will go on a tirade of insults against women. To your face. While you may very well be in hyper advanced Enclave power armour and wielding a plasma rifle.
The same goes for Morrowind. You may be walking around in a daedric armour, with the legendary Big Badass Sword of Doom, be confirmed Nerevar Reborn AKA the biggest Badass in Morrowind's history, who just killed a diabolic demi-god three other demi-gods couldn't handle in a fight. Yet some people still tend to believe they have a chance against you. It's worse if you're a vampire or publicly known werewolf.
Skyrim makes no exception to this trope, Despite equipment, magic, or other abilities, Bandits, Witches, and other humanoid enemies will still charge at you head on, despite you being the only one who can stop the dragons that are currently bringing about The End of the World as We Know It.
Summarized rather well by a popular image that says "Hey, that guy over there just killed a dragon and devoured its soul. Let's go rob him."
A Darwin Award is reserved for the idiot who thought that infiltrating the Dark Brotherhood sanctuary for purposes of journalism was a good idea. Still, the fact that he apparently understood the danger going in puts this example here rather than Too Dumb to Live.
Special mention goes to Rochelle the Red, who decides to kidnap your spouse and hold him/her to ransom — this being the dragonborn, the one destined to essentially kill the Tamriealic equivalent of the apocalypse. By the way, paying the ransom isn't a option.
Amusingly, it's Dragons themselves who are the worst repeat-offenders when it comes to taking on the Dragonborn. Their Suicidal Overconfidence is justified, however, as it is an inherent part of their nature to try to dominate and conquer others. Of course, the Dragonborn's ability to permanently kill them by absorbing their souls hasn't particularly engendered any goodwill or reason why they wouldn't want to see them dead.
A literal example of this is the cause of much of the warring that takes place in Fire Emblem Akaneia. Humanity mistreated the Manakete race (Dragons who took on human form to escape a plague of mental and physical degeneration), despite the fact that they earlier spared them from annihilation by battling against the rogue Earth Dragon tribe, who went berserk due to their refusal to become Manaketes. Eventually, one of them (who, ironically, is the one Earth Dragon who didn't go berserk), gets sick of it, and rallies his likeminded brethren together to put the humans in their place.
Halo 3: ODST plays this straight, and lampshades it, in the audio logs. A man in a car is honking his horn while people run in panic in the streets. A very large man who was giving away kebabs to refugees approaches and leans on the man's car, telling him to calm down and have a kebab. When the man keeps honking, the butcher tells the man "My friend, I am an eight hundred pound man with a large cleaver, who kills animals every day and chops them into small pieces. Do you really want us to be enemies? Or would you rather have a nice kebab?"
In the next log, the idiot still hasn't taken a hint, prompting the butcher to smash his cleaver through the car hood. "Oh! a thousand pardons. But it was either that or smash your windshield, pull you out, and make you into kebabs." After making his point, the butcher finishes the conversation with a polite "...please, stop honking your horn. It frightens the children."
In Portal 2, GLaDOS refuses to turn the insults off even when kicked out of her body and facing a nigh-omnipotent Wheatley, repeatedly calling him a moron and claiming the player did all the work during their escape plan. This gets her (and the player, by proxy) punched down a bottomless pit.
This tends to go both ways in any given Touhou game; early bosses tend to be barely capable of fighting, but insist on attacking well-known badasses anyway, while the last few bosses are you taking on beings that could probably one-shot you if they decided they didn't want to follow the spellcard rules.
Cynder from The Legend of Spyro trilogy gets a lot of grief from Sparx due to being the Big Bad of the first game (though she was Brainwashed and Crazy at the time) who made a Heel-Face Turn. This is despite the fact she's far larger than him and is nearly as powerful, if not as powerful, as Spyro himself. Several other characters also do this while referring to her by her old nickname "The Terror of the Skies". Sure, she's not a gigantic monster anymore, but she's still tough enough she could beat the tar out of them without a second thought if she wanted to.
In inFAMOUS and inFamous 2, if you choose to take the infamous route, then average citizens (even unarmed women) will throw rocks and mock you (an amazingly powerful villain).
In fairness, if you take that route, you kind of deserve it, making it less like bullying and more like standing up to the monster wrecking their city for no real reason.
The reaction of the bad guys in general, especially as the storyline goes on, falls under this. Despite being one of the most powerful Conduits in existence, capable of fighting small armies and giant monsters to at least a draw, and most likely rapidly taking over the city, random Mooks will still show up en mass and try to off Cole.
Averted in the first game by Zeke. He's been taking advantage of Cole's powers since they appeared and so is fully aware of what he can do and even states that he doesn't want to "do anything that might piss (him) off!" after a news broadcast paints him as a terrorist and turns everyone else in the city against him. Unfortunately, his savvy fails him later on and gets him into very serious trouble.
Due to Dude, Where's My Respect? similar to other games, in Pokémon people with 10 level Magikarp will still try to battle you after you are a Champion (i.e. the best trainer in a region) and single-handedly saved the world from disaster. May be justified as the whole point of this game is to get stronger by defeating more experienced trainers. This elevates to Do Not Taunt Cthulhu when you obtain legendary Pokemon. Then you have commoners armed with bugs and squirrels picking fights with a kid who controls demigods that manipulate the fabric of space and time and can usher destruction of the entire world on a whim.
The unarmed generic mooks in Batman: Arkham City will actively taunt Batman if they see him but can't reach him. Made all the more hilarious when you hear prisoners comment about how the last time they met up with Batman he left them with several broken bones.
In Red Dead Redemption during the first mission with Landon Ricketts John Marston is greeted by a trio of Mexican thugs who are hassling him for being an American interfering in the affairs of Mexico. John says that he has no problem with them personally and he is just here in Mexico on official business, he then asks them politely to leave him alone and they can all go home to their families. The trio then continues to harass John and even steals his hat. John then having had enough of their tomfoolery shoots all 3 of them casually and takes his hat back. John by now has killed hundreds of bandits that decided to get in his way so those 3 didn't have any clue who they were messing with. Landon Ricketts lampshades the killings of those 3 idiots and tells John that he becomes like a peasant when he kills peasants and that he isn't exactly endearing himself to the people of Mexico by casually killing men like that. A dragon killing casually when it doesn't need to is just showing off.
In the beginning of Baten Kaitos Origins, some low-ranking Dark Servicemen start taunting Sagi after he's overheard musing over the morality of the assignment. They apparently forgot that Sagi is both a spiriter and a talented swordsman. For extra What an Idiot points, two of the servicemen start another fight with him ten minutes later - while Guillo is backing him up.
Oh, and this is after you killed him once already.
At the beginning of the original campaign, Amie Fern ends up Stuffed into the Fridge after she fires off a magic missile spell at a Githyanki mage who's giving her master Tarmas a hard time. The Githyanki basically rolls his eyes, then one-shots her.
In a rare non-willing example, in Devil Survivor 2, to destroy Alioth's Giant Flyer warship, Kama is recruited to shoot an arrow into Shiva's eye, as he did in a certain myth, so Shiva uses his spear Pasupata to strike Alioth. Problem is, Kama remembers very wellwhat Shiva did to himlast time he pulled that trick, and has to be forced into doing it again. When the time comes, he's also tricked into believing he'd be protected by JP's. Instead, it turns out only his memory would be protected, and he's promptly elevated into the air against his will to the correct angle so Pasupata's attack destroys both him and Alioth.
Max Payne 3: When the bad guys initially (try to) kidnap Max's principals, they could be excused for not knowing how much of a Badass he was. When they attack his principal's office to kill him, specifically because he's killed so many of them, you start to wonder why on earth they're Too Dumb to Live enough to be so bent on provoking him.
The endgame of Saints Row 2 begins when Ultor tries to assassinate the Boss, who has just spent the entire game proving what a Memetic Badass he/she is by almost single-handedly annihilating the three rival gangs that previously controlled Stilwater and essentially taking over the city. (Granted, Ultor's own plans for Stilwater couldn't have worked with the Boss alive and uncooperative, but they don't even try to buy him/her off before sending in the mercs.)
Saints Row The Third continues this. The game opens with the Syndicate attempting to buy off the Boss, Shaundi, and Gat. After a roaring escape out the back of the plane and a dive through the plane when they try to ram you with it, Phillipe thinks the best thing to do is taunt The Boss with the death of a certain companion. It ends with the Boss taking over all of Steelport.
Saints Row IV has an alien general who thinks the best way to deal with The Boss escaping is to blow up Earth. Had he not blown up Earth, The Boss would not have returned to kick his ass up and down the ship.
Star Wars: The Old Republic has this in spades. If you watched all the Jedi/Sith cinematics back to back, it would make a good drinking game counting all the times somebody tells you that, "You're not the first Sith/Jedi they've taken down." One of the most egregious however comes from a small-time wannabe crime boss in the Inquisitor storyline who tries to bully you into working for him after you've single-handedly devastated an entire syndicate that even the Hutts were afraid of.
Numerous citizens in Ultima IX try to bully and pick fights with the Avatar, a heavily armed demigod and messiah of Britannia's religion who's trying to save the world. Despite the Avatar visibly carrying magical weapons and armor, some NPCs will even attempt to fight unarmed, often for petty reasons. The most notable example is a child that starts combat with the Avatar for not giving him money.
Hilariously subverted in Diablo III, where a random citizen in Caldeum tries to rob the Barbarian. The Barbarian's reaction is to ask him to get a closer look, then think again about what he is doing. Cue the would-be robber awkwardly backing off saying he was just kidding.
In Beyond: Two Souls, in which Jodie attends a birthday party, the partygoers end up ganging up on Jodie and lock her in a cupboard. After she escapes with the help of Aiden, she's given the opportunity to either leave or to have Aiden to wreak havoc on the douchebags.
In the second and semi-third games for Baldur's Gate, Edwin Odeisseron likes to boast that he's more powerful than Elminster. His epilogue for Throne of Bhaal reveals he actually was stupid enough to try. He spends the rest of his days as "Edwina", a lonely and bitter barmaid somewhere.
In Bully, other students will constantly attempt to fight Jimmy even though, if the player is doing it right, this consistently results in them lying on the ground moaning. Even the wimpy nerds will, at times, pick fights with you.
The Book of Unwritten Tales has a scene where you literally bully a dragon, in order to help her get angry so she can spit fire and reforge your sword.