Contractual Boss Immunity

The top-level bosses in a game will be immune to the player's most effective or strongest attacks.

Any magician, fighter, or hero with powers, abilities, or weapons that enable him or her to cut through Mooks like butter will rarely be able to use these skills on The Dragon or the Big Bad. In Video Games these enemies will be flat out immune to these attacks, or in the case of a first person shooter be able to take head-shots and keep on ticking, while (annoyingly) players have no such protection from their instant-death attacks. Where's the justice?

The reason programmers and authors do this is for game balance and narrative issues. Where's the big climactic and fun battle if the hero just lops off the enemy's head? A hero who can send the Big Bad into the Phantom Zone, turn them to stone, cleave them limb from limb, or otherwise kill/disable them in less than a heartbeat skirts dangerously close to Boring Invincible Hero.

Basically, they do it because Reality Is Unrealistic. However, this Contractual Boss Immunity ends up resulting in Gameplay and Story Segregation that will really bug players, or worse, harm them if they put a lot of their XP into powering up these abilities. Essentially, this is what puts the "Useless" in most Useless Useful Spells, especially in RPGs.

However, averting this trope can make for a different and entertaining atmosphere. Allowing players to One-Hit Kill any enemy, Cherry Tap even the Final Boss, or characters to use the Five Point Palm Exploding Heart Technique on Bill can be downright awesome!

As you can see, this veers in and out of Acceptable Breaks From Reality. It can be fun to kill a Final Boss with the uber attacks that are normally useless; but it can also be rather boring to do so.

Unrelated to Joker Immunity.

Anime and Manga

 * Is It Wrong to Try to Pick Up Girls in a Dungeon? is an RPG Mechanics Verse, and this trope appears in the final two episodes of the first season. Considering what it took to actually summon that particular Floor Boss, it's no surprise that everyone's usual finishing moves wouldn't work against him.

Tabletop Games

 * In Dungeons & Dragons golems are flat-out immune to spells that allow spell resistance unless otherwise stated, and even then, it usually either slows it or heals/hastes it. Oh, and we can't forget epic-level golems! The Mithral Golem is only DE-HASTED by an actual slow spell, and the Adamantine Golem is straight-up immune to everything (most epic monsters have a ton of immunities on their own). Even this though doesn't stop creative wizards who can bypass the immunities by not targeting the golem itself. Image creating illusions like silent image (mindless creatures don't have the reasoning capacity to disregard out of hand the river dancing gnolls that just appeared), buffing the meatshield and simply "greater invisibility"ing past them are all accepted methods to defeat golems.
 * But then any wizard can bypass SR if they're properly prepared, and there's a ton of spells that ignore SR anyways.
 * There's also the psion-killer (psions basically being wizards using MP instead of Vancian Magic), a golem specifically designed, as one might infer, to kill psions (and by extension wizards/sorcerers).
 * "Thrice-cursed Spell Resistance! It's almost like the universe is trying to deliberately force some form of arbitrary equality between those of us who can reshape matter with our thoughts and those who cannot."
 * Fourth Edition largely averts this by not having a lot of potential instant-kill tricks in the first place. Elite and solo monsters will be tougher than standard ones (to say nothing of minions) and may take less damage from some attacks, but outright immunities to things player characters are likely to use often are relatively uncommon and conditions can be inflicted on these creatures as normal.
 * Paranoia gives certain NPCs "GM fiat armor" as shorthand for "beating this guy would really mess up the plot, so whatever the PCs try, contrive some excuse for it to fail".
 * Feng Shui has this built into the system. Enemies are divided into two tiers: Mooks and 'Named Characters'. Named characters (which include the Player Characters, The Dragon, The Big Bad, and other bosses) have Hit Points and are resistant or flat-out immune to many effects that instantly fell Mooks.

Action

 * In several Metroid games, there exists a "Speed Booster" item that acts as an instant kill to practicaly anything it touches. However, in Metroid Fusion, which was probably intended to be undefeatable, cannot be damaged by it (or by the derived ability called the Shinespark, which has the same effect on enemies as the Speed Booster).
 * Same thing with Screw Attack. It instakills normal enemies but doesn't work on any boss. It is not completely useless, but generally only causes very little damage to the boss and you take some damage yourself or it has to be very precisely aimed (in this cases, though, it does deal MASSIVE DAMAGE).
 * Bosses in No More Heroes are completely immune to regular attacks, unless they are struck during specific times during their attacks.
 * In Cave Story, Curly Brace's Air Tank generates a bubble shield that protects her from A) drowning and B) your Missile Launcher.
 * The bosses of the DLC "special stages" in Mega Man 10 are completely immune to all of the secondary boss weapons (which you automatically receive when you begin the stage). Giving them no special weakness would have been one thing, but it's irritating that you can't even access those weapons' interesting attack patterns doing normal damage.
 * The final boss in In Famous has this in spades. On easy mode all your attacks work, and he can be beaten quickly, and on normal mode your strongest doesn't work, but he can still be killed easily. On the Nintendo Hard mode? At least one of your skills will be below maximum level (assuming you chose an option to get a ton of XP), and all but your NORMAL ZAP and one (relatively weak) evil move work on him. Considering the sheer number of ways he can one hit you if you're at less than full health? Painful fight to say the least. Can take over an hour, not counting the inevitable dozens of retries.
 * The end boss in Prototype 2 has a bad case of this - he cycles between being immune to each of your five attack types without warning, and doesn't let the player fly around or consume lesser enemies in a game based on using mobility, healing breaks and stealth.
 * In the first Syphon Filter, the Big Bad is mysteriously immune to all attacks except gas grenades; this may be a case of Story-Driven Invulnerability. Justified with the second boss, Girdeux, who wears full body armor, except for his flamethrower tank.
 * The sequel's fully-armored final boss is immune to all weapons. Defeating him requires using an auto-shotgun to knock him into a helicopter's blades.
 * The Harmonic Combos of Jade Empire don't work on boss characters.
 * In the Kirby games, bosses and minibosses generally cannot be inhaled, because they're bigger than Kirby. The sole exception is Meta Knight, who is also immune, but is Kirby's size with a cape and armor. In the anime, Kirby tries to inhale him, but Meta Knight just stands still, saying that he has "special defenses".
 * In the Post-Honkai Odyssey mode of Honkai Impact 3rd, quest targets cannot be insta-killed by Back Stabs, but still take more damage than from any standard hit, though, so it's still a good idea to open with one.

Fighter

 * Happens in Soul Calibur III in some Quick Arena battles: sometimes the conditions for winning a match are such that normally powerful attacks become useless or not worth it. This happens even if the attack is known to do 90-100% damage most of the time (matches where an opponent must be bounced off a wall, hit with a soul charged attack, while taunting, etc.). In addition, Bonus Boss Night Terror is capable of flight and can't be defeated by a ring out.
 * Likewise, in Soul Calibur IV it's not uncommon for bosses and tougher enemies to be equipped with the Auto-Grapple Break and Auto-Nullify Ringout skills.
 * In Guilty Gear XX AC, you can't activate an instant kill move against the final boss, much as you'll want to.

First-Person Shooters

 * Firestarter gave special abilities (aka Artifacts) that gave a significant boost. You couldn't use them during boss fights, but special abilities already in use (incuding one that slows all enemies) weren't stopped.
 * In Heretic and Hexen, if an attack would guarantee a one-hit kill or render the enemy as good as dead (such as by transforming them into something weak), boss monsters are either completely immune to it (in the case of special effects) or take a negligible amount of damage (in the case of literal one hit kills).
 * On the subject of the engine, the  of Doom 2 is outright invincible to every weapon except the rocket launcher. INCLUDING the BFG-9000. It is only that specific boss, though - you can kill the  in the original game at point blank with the BFG with one shot.
 * In the first two Turok games, the Nuke Weapon is useless against bosses. It can, however, be used to destroy Primagen's flyers at the end of Turok 2.
 * Deus Ex Human Revolution: The bosses you have to kill usually can counter Takedowns. Jaron Namir is an exception, but only if you catch him immediately after he does a wall-mantle.
 * Sanchez, the first boss-type enemy in Soldier of Fortune II, is immune to bullets and can only be killed by electrocution.

Role-Playing Games

 * Eternal Darkness really only has two true boss battles. The first is immune to bullets and impossible to reach with melee attacks and has to be killed by magic cast at just the right times. The second is mostly immune to everything, except assaults on his relic of power and attacks from spirits of those who came before. Until the very end, of course.
 * Boss-type creatures in Albion are immune to most paralyzation and disintegration spells. There is one spell of each type that circumvents this immunity, potentially making the game Unwinnable, as one of the bosses carries a Plot Coupon that gets disintegrated along as well. The last boss is immune to everything (except Steal Life and lightning based spells), but you don't have to actually beat it.
 * In Baten Kaitos: Eternal Wings and the Lost Ocean, every single boss in the game is 100% immune to every status effect; the only exception is the two tentacles used by the Tree Guardian in Anuenue, though the boss itself is still immune.
 * This is changed in Baten Kaitos: Origins, where many bosses are weak to knockdown, freeze, burning, etc. However, instant death, sleep, and stun still do not work.
 * In MMORPG City of Heroes, Arch-Villains and Heroes (essentially big big bosses) have a system of resistances to controlling effects such as slows, stuns and immobilizes so high that they are all but immune. This presents a significant problem for characters who specialise in these effects, ranging from forcing them to game the system or use their secondary abilities, to making them outright powerless.
 * This is referred to as the "Purple Triangles of Doom" because of the aura of purple triangles floating around the Archvillain's head. When they point up he has magnitude 50 protection against most status effects on top of the magnitude 6 protection that he would have as a normal Elite Boss. When the triangles point down, then he only has the magnitude 6 protection. This up and down cycle is not very obvious with all the other visual effects going on during battles, so usually nobody notices that they are down unless the Archvillain is suddenly locked in a Hold. For reference, your average status effect tossed around by the player will at most have a magnitude of 3.
 * The vast majority of Final Fantasy bosses are immune to any form of instant death attacks, status effects, and Percent Damage Attacks. There'll occasionally be one or two bosses in a game that the spells will work on, to reward players that Try Everything, and there's frequently a slots combination that'll kill anything, though.
 * Surprisingly, in the original Final Fantasy I, it is possible to defeat elemental fiend Tiamat simply by having a Black Wizard cast Break on her and turn her to stone.
 * In addition, the final boss can be killed by casting Bane, a One-Hit Kill spell. It doesn't always work, although that's no problem since you can infinitely cast Bane using the Bane sword as an item.
 * Final Fantasy IV has the Dark Elf, a challenging midgame boss, unless you cast Weak on him, which drops him to single digits. This weakness was removed in the remake.
 * There's a glitch in early versions of Final Fantasy VI that can let you use instant death spells on bosses. There's still a boss vulnerable to X-Zone in recent versions, but he's supposed to be.
 * Odin's Zantetsuken in Final Fantasy VIII occurs randomly at a battle's start and will instantly kill the enemies unfortunate enough to get in its way, but when it occurs in a boss fight against Seifer, Odin himself gets killed.
 * In Final Fantasy V and Final Fantasy VII, Odin can be used to kill mooks instantly, but against bosses he will perform a powerful damaging move instead.
 * On the other hand, Final Fantasy VIII has Selphie's hard-to-perform Limit Break "The End" works on bosses, including the final boss Ultimecia. Also, the boss Abadon, being a zombie, can be killed simply by tossing a Phoenix Down at it or casting Full-Life.
 * Final Fantasy X gives us Yojimbo, who can perform One Hit Kills on any enemy, be it random encounter, final boss (not that you need it), and all the bonus bosses with his Zanmato move. However, this requires either understanding a farcically complex mathematical formula, or giving him more than half your money.
 * Geno Whirl of Super Mario RPG does 9999 damage when done with a frame-precise timed hit. All enemies have less than that; the Final Boss has 8000 HP. Most bosses are immune to this attack, however, save for one.
 * Adventure Quest made a marathon Bonus Boss immune to elemental-resistance-shuffling after someone figured out that they could use a class ability that dealt percentage-based fire damage, and the monster's 1275% energy weakness, to one hit kill an Eldritch Abomination. It dealt billions of damage.
 * See also the ones that are immune to Power Word Die.
 * In Mass Effect 3:
 * You have The Dragon Kai Leng  In addition, Stasis will never work on him, even though he is unarmored.
 * At one point in the game you have to chase an enemy boss . While you and your teammates have an assortment of powers that should slow down or stop that boss enough for you to easily catch up, none of them have any effect.
 * Moraff's World and Dungeons of the Unforgiven (Roguelike RPG of approximately 1990) have the Holy/Nuclear Hand Grenade which instantly kills the monster. Usually. Bosses catch it and give it back to you. If you try any instant kill/disable spell - they say right away that it won't work.
 * In Pokémon Mystery Dungeon the player is not allowed to use Orbs in a set boss battle, probably because things like the One-Shot Orb (that does exactly what it sounds like) and the Itemizer Orb (which turns an enemy into an item) would make it too easy.
 * Oddly averted in the case of Stun Seeds, which can render bosses incapable of doing anything until they're damaged or a huge number of turns pass, thus giving you plenty of time to strengthen yourself with supportive moves or pick off their minions without them bothering you, which can turn an otherwise difficult battle into a cakewalk.
 * The boss of Septerra Core was immune to insta-kill attacks and only flinched on high-power attacks. However, using the cloak spell prevented him from landing his one-hit party-kill attack against any party member.
 * Shin Megami Tensei Nocturne contains 5 elements for inflicting stats aliments (mind, nerve, death, expel and curse). that can all inflict various standard stats effects all but 2 bosses (Forneus, who comes before the first instant death spell and Troll, who is weak enough to be a miniboss at most) are immune to death/expel and all but a handful of early bosses null or strongly resist the other 3. Most of the instant kill effects do work well on various flunkies however.
 * Shin Megami Tensei is unusual for a JRPG in that only bosses are outright immune to instant kills and incapacitating spells. All other enemies will be vulnerable to at least some of them, and in a good number of cases outright weak, translating to "one cast, one kill" against those types of enemies. As far as general gameplay is concerned, instakills are definitely NOT Useless Useful Spells (Being MegaTen, simply "attack"ing a random counter is a good way to die). Also, stat debuffs definitely do work on bosses (and are seriously necessary in most cases).
 * In Persona 3 and Persona 4, instant kill spells return as Light and Dark magic. Some enemies can block either or both elements, but every boss is immune. This hits no-one harder than poor Naoto in Persona 4. Naoto specialises in Light, Dark and Almighty magic, which is great for mowing down large numbers of Mooks but utterly useless in boss fights.
 * The day 7 boss in Devil Survivor 2, Benetnasch, has a passive "Pacify Human".
 * Bosses in World of Warcraft tend to be immune to incapacitating effects such as Polymorph, Interrupt and silence effects, and most notably stun effects. This is quite necessary, as if they weren't, every party would simply take as many rogues as possible to keep a boss stun-locked and incapable of doing anything. Similarly they're almost always immune to slow, to prevent them from being kited to death. There was a boss in The Burning Crusade whose movement speed was slow enough to allow kiting, and on heroic difficulty some people did indeed refrain from ever getting close to it.
 * Bosses are almost always immune to silence, and some of their spells cannot be interrupted, though others can be, and indeed interrupting them can be necessary. Lady Deathwhisper's is a good example with her interruptable frostbolt of Kill the Tank. The game is helpful enough to provide a shield around the cast bar of uninterruptable spells so people don't waste an spell. A few spells also simply have a different effect on them (most notably the Deep Freeze spell of Frost Mages). And they are fully vulnerable to attacks or spells that can only be used on targets with low health or do more damage in that case. Those skills typically kill of a normal enemy right away, but against a boss they are still valuable, especially against the kind of boss that is the most difficult at low health.
 * Most bosses in the Dragon Quest series are immune to most or all status effects. Many of those that aren't immune to all of them can be made hugely easier by application of one they're not (For instance, a Troll King in Dragon Quest III can be made trivial by silencing him so he can't cast his attack-buff spell), and virtually none are immune to effects that directly decrease their stats—although a very rare few can nullify such effects after they're cast, for most bosses, these spells are outright essential—and even for the ones that can nullify them, they have to waste a round doing so.
 * For that matter, Random Encounter enemies are rarely, if ever, immune to status effects, and like in Shin Megami Tensei, some of these can be very difficult, such that simply going "attack, attack, attack" is little more than a way to get yourself killed.
 * In Neverwinter Nights, it shows the results of the in-game die rolls on the game journal. It gets rather annoying when you see "Player casts Hold Person. Boss attempts Will save. Fail!" while the boss continues to attack.
 * In most Ys games, the Big Bad is immune to the Infinity+1 Sword.
 * In the Golden Sun games, bosses seem to be immune because of how the Luck stat works: Luck increases a creature's chances to resist status effects. Since every boss in the game has a Luck stat of around 50 (or higher), their resistance to these effects is extremely high. Some of the Djinn attacks are able to bypass the resistance, though (mainly the ones that work like a Silence effect).
 * Subverted in the rogue-like Ancient Domains of Mystery. Many of the game's most difficult bosses can be rendered impotent if the player uses confusion, blindness, darkness, poison, or stun on them.
 * The only way to truly get rid of a Nethack monster is to dispose of its corpse. The Riders have special coding that makes getting rid of their corpses nearly impossible and they are more than likely to revive under your disposal efforts. The Wizard of Yendor is similar as, after you have stolen a McGuffin from him, he will constantly revive no matter how many times he is killed and will make the remainder of your game miserable.
 * Mostly averted in Xenoblade Chronicles, where the only thing bosses are universally immune to is instant death.
 * Subverted in Monster Girl Quest Paradox. While bosses are more status-resistant than normal enemies, they never have blanket immunity to all status effects. Even Bonus Bosses are vulnerable to one or two, and many strategies for defeating them exploit this.

Shooters

 * Some games, usually on-rails shooters like Star FOX, have area-effect attacks designed to destroy all on-screen enemies, but will only significantly damage bosses.
 * It's very common for Bullet Hell shooters to have the Bonus Bosses and/or True Final Bosses become invincible when the player bombs, taking no damage from the bomb or any of the players shots until the effect of the bomb ends. Generally, a barrier of some sort will be placed around the boss to show when this is occurring, although other things have been known to occur to indicate that the boss simply is not taking any damage (for example in ESP.Ra.De the boss literally leaves the screen). Sometimes the standard Final Boss gets this type of invincibility as well when they're on their final pattern. CAVE and Touhou Project games are prime examples of this.
 * A few weapons in the PlayStation 2 Ratchet and Clank games. The Zodiac and RYNOCIRATOR are one-hit weapons against normal opponents, but take off very little if any HP from bosses.

Stealth

 * In Assassin's Creed II all generic enemies are vulnerable to your Hidden Blade (and in particular to being counter killed), but the penultimate and final boss are conveniently immune.
 * Also played straight in Assassin's Creed: Brotherhood: In addition to breaking free of grabs, the Kung Fu Proof Mooks and mini-bosses also can dodge or outright block counters; the final boss can as well. (There are two more story targets, but they're not so much bosses as "guys you have to kill without being detected, or mission failed.")
 * In Metal Gear Solid, you can't break bosses' necks, nor can you slit their throats, and the KO is just minor incapacitation.

Strategy

 * Command & Conquer plays this straight; in the GDI campaign, you can't one shot the temple of Nod with the Ion Cannon. The rest of the series made sure you can't knock out the superweapon building or construction yard with only one superweapon attack, but the rest of the base used to power these weapons were fair game.
 * Tiberian Sun's expansion Firestorm had a curious glitch in the last mission of the game. While a single Ion Cannon blast won't destroy the mission objective, it can destroy the firestorm generator protecting it. Doing so bypasses the entire sidequest of having to capture the relay stations to shut the core off. In addition, while the Core Defender is resistant to all attacks, it was still programmed as a base land unit, so if you destroyed the bridge it was on while it was over water, it just dies due to the game not knowing what to do with a unit dropped into water.
 * In the Turn-Based Strategy game Luminous Arc 2, anyone that is equipped with the Auto-Medic Lapis is completely immune to status ailments. Most, if not all, bosses are equipped with Auto-Medic. The player can win Auto-Medic Lapis as well, allowing your characters to get in on the fun.
 * Cyrus in the Dawn of War II campaign gains an ability to use his sniper rifle to instantly kill any infantry unit. While it makes sense that it doesn't work on vehicles or Monstrous creatures like Carnifexes, it makes less sense that it doesn't work against bosses which are just more powerful infantry units (though it does do a lot more damage than his regular attack). Bosses are also immune to stun and knockback effects in the Dawn of War II campaign, making it impossible to disrupt them; this is removed in the expansion Chaos Rising, where most bosses, particularly infantry, can be stunned and knocked around at your leisure.
 * The final four bosses in Fire Emblem: Radiant Dawn all come equipped with either the Nihil or Mantle skills, which prevents attacking units from using their own skills against the boss (and in Mantle's case, Critical Hits). This is mainly to prevent them from being quickly dispatched by the Mastery Skills, many of which can reach ridiculous amounts of damage when used by a high-level character with an SS weapon. The majority of other bosses are still vulnerable to them, however, and the player even gets a few Nihil scrolls of their own.
 * Assassins, in the games that have the class, are able to randomly kill their opponent instantly, even if the attack would otherwise have dealt 0 damage. In the GBA games everything but the final boss is fair game to be assassinated, but as of Path of Radiance, all enemies classified as bosses have contracted the immunity.
 * In Final Fantasy Tactics Advance, bosses and some leaders of enemy armies usually have ribbons marked by their names. Said ribbons make them immune to the laws that are constantly hounding your own characters (and any enemies without ribbons by their names). Characters who break the laws badly enough are carted off to jail - a "mission failed" scenario if it happens to main character Marche - and enemies without ribbons will never deliberately break the laws. But thanks to the ribbons, bosses can (and will) do anything they want without penalty.