Ridley is the Metroid equivalent to Death from Castlevania - a recurring boss that always makes you want to hurl a controller. To make him even more like Death, when he turned out to be a pushover in Metroid: Zero Mission, fans complained. He WAS hard in Super Metroid, though. Part of what makes him stand out is that while all other bosses have weak points that you can target and fairly predictable attack patterns, there is no trick to fighting Ridley other than to drop his HP to 0 before he does the same to you, and he has a lot more HP and attack strength than you do. And then there are Self Imposed Challenges. Low percent runs or even sequence breaking for the hell of it makes him hard as you have to dodge all his attacks and try to replenish your supply of missiles with a beam that only goes a few pixels.
Metroid Prime had a cruel bait-and-switch version of this. At first, it just seems like Ridley's gonna fly around, bombarding you with easily-dodgable lasers and missiles. Then, when you get his health down to a quarter, his wings burn off and he shreds through your fifteen Energy Tanks like tissue paper.
And in Other M, he's not only as melee-happy as he is in Prime, but he also goes invincible at times. The only way to make him vulnerable is by use of a Super Missile, which requires you to go 1st-person and stand still, locking on to him for two seconds straight while he's still attacking you.
The (aptly named) Nightmare in Metroid Fusion caused more than one Game Boy Advance to go through a wall. Aside from the huge amount of damage it does to you every hit, it also can inhibit your movement by manipulating gravity.
There's also the BOX Security Robot. Both times you fight it, you have to hang from monkeybars on the ceiling and shoot down into its core, which is easier said than done. It can't be hit when it attacks, and its attacks are all designed to knock you off the ceiling to get trampled by the thing. Just to add to it, the second fight takes place above a pool of electrified water, which knocks your health off very quickly.
Yakuza the Kung-Fu Spider. Its first form zigzags across the boss room, trying to grab you; if it grabs you, it'll suplex you for staggering amounts of damage. Thankfully, if you wiggle enough you can sometimes break away before suplex-spider makes you into a pancake. It's only vulnerable at certain times (namely, when it spits fireballs). After you blast its legs off, it gets much easier, since it loses the suplex attack, gets much easier to hit, and only spits weak projectile attacks.
The final showdown with SA-X? It's a fight against an exact duplicate of your character that attacks relentlessly with all of your devastating special weapons — except that it can take a lot more damage and has the superior dexterity of a computer. Winning this encounter comes out to learning how to screw with the AI.
Although it takes less damage than the other bosses, the Omega Metroid can become this if you're not perfectly on time - it deals massive damage, and its attacks cause you to stop for several seconds, which wouldn't even be that bad if you weren't on a timer. The only real way to win is, ahem, touch it real quick and go.
Thardus is just dang huge, and thus its attacks hit like a train made of boulders. Most of the time it's throwing boulders at you or curling up and rolling around the room, where it's very hard to dodge because of its size. To damage it, you have to switch to the Thermal Visor, shoot out the highlighted boulder in its body, switch back to the normal visor, and continue blasting away at the highlighted boulder. You have to do this a lot. And as the fight goes on, it summons a snowstorm that makes it impossible to see more than 10 feet away, which makes it a whole lot harder to dodge its rolling. Annoying and long enough normally... Hard mode is a whole 'nother beast.
The Omega Pirate is a massive Elite Pirate found at the bottom of the Phazon Mines. For starters, the room has several pools of Phazon in it that are extremely easy to accidentally walk into when you're trying to avoid the Omega Pirate. He's also good at backing players into corners and smacking them for ridiculous amounts of damage, and while you can stun him with Power Bombs, it's hard to get away without losing a lot of health. Even worse, he spends most of the fight with a shield up that blocks all weapons except Missiles (and the Flamethrower). Damaging him requires you to jump through a bunch of hoops; first, you blast off his shoulder and knee armor, then he vanishes and summons several Beam Troopers. As you fight the Troopers, you have to listen for the sound cue that tells you when he reappears in one of the Phazon pools, which allows you to hit the heart, the only place he can be damaged. On Normal, this is all fairly manageable, but he's a nightmare on Hard. Quite aside from his boosted damage and massive health bar, the Troopers that he summons become a major threat, especially the Wave Troopers.
Meta Ridley. He starts out almost hilariously anticlimactic, flying around your platform and throwing bombs, missiles, and lasers at you, all of which are easy to dodge. Then, you get him down to about a fifth of his health, and his wings burn off. He lands and goes into melee mode, where he lunges at you and takes off huge amounts of health with every hit. He also gets much harder to damage, and has to be stunned with a well-timed missile before he exposes his weak spot.
The Hive Totem is either a simple Warm-Up Boss or That One Boss, depending on the player. You fight it on a small pedestal in a room flooded with Grimy Water, which is difficult to get out once you've fallen in. The Totem is a stationary mech at the far end of the room that releases wasps, which fly around you in sync and stop to ram you. Defeating the wasps opens up the weak spot on the Totem; there are four weak spots to destroy. Now do all this with a max of 99 health and your basic Power Beam.
The Spider Ball Guardian is a nasty, confusing Puzzle Boss. The battle is done in Morph Ball mode and involves setting traps for the guardian. The problem is, several of the traps are nearly impossible to reach without minute precision. In addition, a design oversight makes the final area of the fight much more difficult than it should be; several of the Bomb Slots you need to activate are located at the top of slight rises, meaning it's very easy to overshoot the mark, wasting the small window of time you have to activate all three.
The Boost Guardian is just aggravating. The fight takes place on Dark Aether, outside a safe zone, which means constant, steady damage. The fight takes place in a tiny confined little room. Every so often, the Guardian will shift into a little sphere and rocket around for far too long, careening into Samus with alarming frequency and accuracy. It's completely up to luck however often he hits you. You can go the fight, not get hit once, and then get ripped apart when you've got him down to a quarter health. In addition, it's possible to come out of the fight with too little health to get to a safe zone. It's unlikely, but there's nothing more soul-crushing than having to go through that fight twice.
The game gives you some Boss Arena Recovery in the form of four little pillars that yield 100 energy when destroyed. The problem is that only the Boost Guardian's ball form can destroy them. Sometimes, it'll refuse to touch them when you're down to twenty energy and about to die, other times it'll smash all four of them in the first five minutes of the fight and deny you recovery. Also, the destroyed pillars spawn Inglets infinitely.
The Boost Guardian and Spider Ball Guardian are so infamous for being difficult that, when Metroid Prime 2 was ported to the Wii, they were the only two bosses who were made easier.
While typically not quite as difficult as the Boost Guardian or the Spider Guardian, the Power Bomb Guardian can be pretty frustrating. To beat the boss, the player needs to crawl up a maze of Spider Ball tracks to four activate different bomb slots. After activating one, Samus falls down and has to climb up again, and all the while the boss is shooting Power Bombs at you and Inglets are spawning everywhere shooting globs of darkness at the player, both of which will damage and cause Samus to fall. It is only possible to climb the rails in the Morph Ball, so any gamer will be defenseless against the Inglets unless he or she can coax them into the range of one of the boss's Power Bombs. And the Power Bomb Guardian will often throw power bombs in front of Samus' path, giving her only enough time to roll away before being hit. Forget trying to avoid them if you're on a small strip of magnetic rail.
And then there's Emperor Ing, the brutal three-form final boss fight. His first form is a massive, immobile creature in the middle of the room that attacks with his tentacles. Destroying the tentacles exposes the eye, the Emperor's weak point. The second form is a cocoon you have to attach to with the Spider Ball and roll all over to bomb its weak points. This form is kind of a breather, since Emperor Ing only has one easily dodged attack. There's also Inglets crawling all over it, which can be killed for pickups. Finally, you have the third form, a gigantic Warrior Ing. He jumps around like a flea, makes huge shockwaves, fires beams everywhere, and gives virtually no opportunities to regain lost health unless you run low on ammo. He's also yet another Barrier Change Boss, constantly swapping his weakness between light and dark, and requiring you to use the Power Beam to render him vulnerable at all.
Amorbis, the guardian of Dark Agon Temple. Their burrowing forms aren't particularly dangerous, but they're hard to track and like to pop out underneath you. After you break the armor of the burrowers, they attach to the alien sphere in the center of the room and gain several nasty projectile attacks, one of which shuts off your safe zones and another one that turns them invincible for a short time.
Chykka, which goes from "alright" to "JUST DIE ALREADY", is an irritating, long boss. The first phase is easy enough, but then it goes downhill fast. The strategy for the adult form sounds simple at first- "stun it and shoot the wings from behind"- but turns into an exercise in patience. The thing darts around to the point where the only way to even have a chance to hit it is to spam normal shots, since the shots are pathetically slow (or spam missiles, hope you've been collecting expansions). If that sounds hard enough, there's still some attacks that are tough to dodge (and the seeker missiles are a charged attack so you'll want to dodge). Once the thing finally goes dow- just kidding, it still has most of its health. As it goes down, it releases a huge water wave that is almost impossible to dodge without jumping well in advance. Then it comes up as Dark Chykka. Welcome to the longest boss fight until the final boss in the game. Oddly, this phase is easier than before, since it doesn't dart around at all and the best strategy is to shoot its inflated eggsac with charged Light Beam shots. Even after it comes back up as normal Chykka, it still has half of its life left. It gains new attacks, especially where it flies around, almost impossible to hit. Repeat again, and the thing finally dies. Let's face it, Torvus Bog is full of Those Bosses.
Alpha Blogg. On Normal, this fight is tricky, but doable; if you have enough energy tanks, then once he Turns Red and gets faster, you can tank his attacks and attrition him to death. On Hard, however, turning it into a war of attrition will get you killed; you have to be able to damage and dodge him consistently, even when he gets really fast.
Grapple Guardian, which isn't so much hard as just aggravating to hit at all. First you need to target its eye and damage it until the boss gets enraged. The eye is rather small, but mercifully is easy to hit. Expect to either spam your basic power beam until your finger hurts or waste your precious light/dark ammo, however. Once you hit it enough, the Grapple Guardian fires the eponymous Grapple Beam at you. If you get hit, you'll take damage as you get closer and closer to it. If it misses completely, you're soon back to the eye phase, during which it takes no "real" HP damage. The trick is to stand behind one of the electrified pillars in the room and let the boss stun itself by grappling it. Once it does you can hit its back, but by the time you've run/jumped behind it you only have a second to act. Firing a Super Missile (as you will want to do) takes almost precisely this amount of time. A 5-shot spread missile is a bit faster, but takes time to lock on instead. Charged beam shots also work, but either drain a lot of ammo or leave you with very little damage dealt. The boss actually gets easier when it Turns Red later, since the process for hurting it becomes a lot quicker.
Metroid Prime 3 has Gandrayda. Whenever she hasn't taken on the forms of previous bosses/enemies, she jumps around so fast and so much that it's nigh-impossible to reliably hit her; she also tosses explosive energy projectiles and can and will try to jump on you, draining valuable health unless you can quickly shake her off. The first half of the battle is easy, the third quarter is more challenging but still okay, but in the last quarter she abandons the shape-shifting completely, making her extremely difficult to hit, alternates between invisible (which requires you to change visor) and hypermode (which jams the visor and forces you to go hypermode yourself to damage the boss, which can become a problem if your health is already getting low), and it's very possible to accidentally step into the highly damaging acid rain. Also, the only way to regain health is in the first phase.
Rundas is no slouch, either. He'll speed around the arena while semi airborne, where it's very difficult to hit him with your slow shots and the giant ice pillars he sets up specifically to give himself cover. He also packs highly damaging ice attacks that can freeze you. His hyper mode makes him even faster and can lead to an attack where he swings around a giant icicle like a flail and throws it at you, which highly damaging, capable of tearing off energy tanks at a time unless you attack him enough times or hard enough in the short period before he throws it. And to make things worse, you will most likely only have about 3 Energy Tanks at this point.
Special mention goes to Mogenar, which becomes a long ordeal on higher difficulties. His weak points are protected by spheres that he can recharge, and on the highest difficulty, they are very hard to destroy, the recharge is nearly impossible to prevent completely, and you'll likely need to destroy each sphere at least twice before you can destroy the weak point underneath. And he has 4 of them. And the last one is on his back, so the only way to get to it is to make him charge into a wall and dump a Hyper tank into him while he's looking around. Not that you have any energy to spare, natch - 4 tanks, maybe 5 tops, is about all you can have at that point in the game, and you can't go hyper without having at least one full. That said, with a little practice Mogenar gets easy... except for the part where you have to bomb his shoes off. This requires you to get into morph ball form after jumping over a shockwave, but before he manages to step on you, then planting perfectly timed bombs.
Dark Samus is a fairly tough final opponent on Normal. On Hypermode? She's unabashedly sadistic. It mostly has to do with the health system you use during the battle, which essentially acts as a combo timer/hit counter, but her attacks are still a pain to dodge and she loves to spam them. And if by some chance you get to AU 313's head, it becomes nigh impossible. We're talking four different attacks, and they all take a major chunk out of your remaining energy. At least Dark Samus gave you health pickups...
The Slench in Metroid Prime: Hunters. Not only are they hard as snot to hit when their giant eyes start flying around, but killing all of their tentacles in order to damage them in the first place is frequently an ordeal in and of itself. The worst thing of all that the eye is moving so fast, and only the pupil will take damage, and you don't have any targeting system to lock on it. It gets even worse when you reach the Slench v3.0, which is positioned at a very awkward angle, and the Slench v4.0, which is on the ceiling and starts rolling after you when you kill all its tentacles. After defeating it it's advisable to take a long rest. (To make matters worse you have a timer after each boss battle... at least it creates a checkpoint after you defeat the boss so you're not forced to kill it again.)
Every playthrough of Zero Mission can be a massive hold up on that stupid Zero Suit Chozo boss. The first 3 hits are fine, but the last is nigh impossible to hit due to lack of time frame, and if you're too late it'll hit you instead (that's what it does whenever it doesn't flash vulnerable and it just gets annoying after a while). Let's have a little clarification. Near the end of the game, you fight one of the last remaining Chozo artifacts. To defeat it, you need to shoot it four times when it's vulnerable. At any time when it's not vulnerable, it will show mirrored image of Samus, and shooting it will cause her to take damage instead. Sounds simple, right? Don't get used to it. Once you've lowered its health a bit, it will float around the room in increasingly erratic patterns, hoping to do you in via Collision Damage. It also drops lightning bolts that crawl across the floor and ceiling. So, the final score? It flies around randomly, it hurts to shoot it sometimes, and it makes the environment you face it in lethal. Have fun!
On Hard, the difficulty spikes considerably: the boss itself and its movements don't change, but because Hard Mode halves the total amount of energy you can pick up (energy tanks now only give you half a full unit apiece) and raises the damage that enemies do, you have a maximum of four and a half full tanks at this point in the game and the boss now does a full energy tank with every hit. Luck will be a factor in your success.
As you're facing it down, the Metroid Queen in Other M will spawn a normal Metroid; the only way to kill said Metroid is to shoot it with a charge shot to freeze it, and then aim at it (pointing the Wii remote at the screen and being locked into a stationary first-person perspective) while you charge up and fire a super missile at it. Not a problem until the she starts hemorrhaging so many Metroids that it becomes impossible to freeze some Metroids and charge up a super missile without getting snagged by other Metroids, unless you freeze ALL of them before the first one you froze in the sequence wakes up. This gets easier if you know you can use the 1 button to hold onto a charge when going into visor mode, but still. There's no special tactic, just using sense-move at the last second, firing at the clusters and hoping to god your energy doesn't get too low, because if it does, you're fucked, considering you won't have time in this battle to use Concentration before a Metroid head-rapes you. Then in the second phase, it tosses out heavy-hitting attacks that are almost impossible to dodge. And then the third phase makes you use a technique that you haven't been allowed to use (and don't even know you can use) since the opening tutorial eight hours previous, within five seconds or you die. Joy.
There's the Rhedogian (that flying anomalocaris thing), which you have to fight four(six if you count the mini-boss rush after the end) times. He's really freakin' fast, dodges nearly anything, does heavy damage, has hard-to-dodge attacks, and is invincible most of the time. Also, the first two times you fight it, you have barely any room to maneuver around, and the second time you can get a Non-Standard Game Over if you take too long (read: don't know what to do) before getting to him. The second battle is probably the worse, as you're stuck in a very confined space with him, so he becomes really difficult to dodge. On Hard, your success depends on when he will try to shoot a giant laser at you. Thankfully, after the third time around you get the Screw Attack, which makes him significantly easier.
Goyagma, in a Wake-Up Call Boss sense. Faced just after a hellish sequence without the Varia suit, Goyagma is easy enough to hit and damage, but his attacks are very unpredictable. He has long arms which he slices across the platform you're on. Sometimes, he'll do it twice. Unfortunately, it can be very hard to tell when to jump as sometimes he swipes slow and sometimes fast, with little to no indication and so you may jump too early or too late. Later in the battle, one of his attacks is a constant hand smash to avoid - but it also forms a mini-eruption where you're at, so you have to get ready to dodge that quickly too. Near the very end, he will do the mini-eruption thing, THEN very quickly follow up with a fast swipe. You won't see it coming. In Hard mode, each of these attacks do 1/3 damage. So that's 1/3 for each mistake, and it's hard to predict against.
The RB176 Ferrocrusher on Hard. Its speed is absolutely insane, and it hits like a sledgehammer. It has a laser which causes explosions wherever it fires. It will grab you with its arms and drill you into the wall for a One-Hit Kill if you even get close to it. Its charges are very difficult to dodge, and take off massive chunks of your health. Down to the last of your health and need to heal? Too bad, you won't even get a chance until you survive its second phase long enough to freeze its wheels. Insultingly, the pilot's identity is never revealed, leaving the plot point of the Deleter hanging.
Remember the Nightmare? It's back, alright, and still just as nasty. Most of the fight takes place in high gravity, which makes you run at a snail's pace, makes your missiles worthless, and you're stuck on the ground for a few moments after landing from a jump; all while Nightmare is spamming energy projectiles and giant lasers from its arms. It's also invincible until you disable its gravity manipulator (thankfully your shots home in on it), since you can't hit it with missiles in high gravity. Once you've dealt some damage to it, it may start sliding or walking along the ground, which, if the gravity is on, requires you to jump to a lower level to avoid it. Thankfully its second form is pitifully weak (you're immune to high gravity, it can only shoot painfully slow energy balls and form gravity wells, and sometimes it just lays there on the ground).