Yuuka in Stage 5 has the Master Spark (yes, the original Master Spark, before Marisa copied it). Your only warning is a thin line going down the screen that lasts a split second, and unless you've seen it before you will get killed. Even once you know to dodge at the sides of the screen, the bullets that accompany the laser are fast, and hard to see because the screen is so brightly lit.
In stage 4, while fighting a Dual Boss, players have a choice as to whether to fight Yuki or Mai in the second phase. Mai is usually cited as the easier of the two to fight, since Yuki's attacks tend to be more difficult, more random or fast and have many more bullets. Yuki's That One Attack is her third phase, which is an attack with a very large amount of health that lasts a long time, and basically spews very fast bullets chaotically all over the place, filling the screen. Inexperienced players who can't react or dodge fast enough will go through a lot of bombs or lives on this spell, since the health bar is large.
Embodiment of Scarlet Devil
Cirno, of all bosses, gets one: the unnamed "ice shotgun" attack she starts off with in Stage 2 of EoSD. You're forced to make wide sweeping motions across the screens to avoid it (unless you can react to rapidly-moving patterns fast enough to weave through it), lest you waste a bomb or two.
Ice Sign: Icicle Fall -Normal- becomes this for anyone who is used to what it's like on Easy. In the Easy version of the attack, there's a glaringly obvious safe spot directly in front of Cirno, as well as in the area above her. On Normal, attempting to take advantage of those same safe areas is almost guaranteed death, due to the addition of several large, aimed bullets fired in your direction from Cirno's position, which are designed to punish any players that try and use the old safe spots.
Remilia Scarlet mostly averts this on Normal, but on higher difficulties, she gains TWO of them. Scarlet Gensokyo, her final card, is notorious for having its bullets spreading at incredibly awkward angles, and sometimes spreading them completely at random - and since it's a final card, it has a ton of health and bombs don't do anything against it. Due to its randomness, it can even outright wall the player, making dodging it impossible. And then there's Scarlet Meister, which is even WORSE; it's often cited as the single hardest spellcard in the entire Touhou series.*
Gengetsu's timeout phase isn't something faced in normal play, while Scarlet Meister is.
Notable in that it gets this reputation despite not appearing on Normal difficulty; it's impossibly hard even by Lunatic standards.
Perfect Cherry Blossom
For the Prismriver Sisters in stage 4, we have Merlin's opener, featuring curving and homing lasers with movement that is extremely hard to read. The attack is so bad that the fact that only Sakuya has to face it is the single greatest argument against playing as Sakuya, and more than a few players pick Reimu purely for this reason.
Lunasa is bound to destroy you if you've never played Perfect Cherry Blossom on hard difficulty. After the sister's first collab spell card, the girl who got the most damage will attack you solo before them going collab on you again. Lunasa's solo spell cards for Easy, Normal and Lunatic difficulties are the easiest thanks to them being slow-paced and predictable; however, her Hard spell card develops into a fast-paced barrage of night-unavoidable bullets. Extra points because it starts the same as the others, just so you expect slow-moving micro-dodging.
Yuyuko's Deadly Dance releases several bubble-type shots that track you down while smaller butterfly danmaku rotate and cover most of the screen. This wouldn't be a huge problem if the bubbles weren't larger than the norm and therefore cover enough of the screen to hide some of the rotating danmaku.
Also, her last non-survival card "Perfect Cherry Blossom of Sumizome" is a confusing mess of aimed butterflies amidst smaller falling "cherry blossom" bullets, and like most final cards, it has a lot of health.
And then there's her survival card, Resurrection Butterfly, which is sixty-six seconds of surviving against waves of butterflies, the red waves of which fire at fast criss-crossing angles that are extremely hard to read.
Ran Yakumo has "Charming Siege from All Sides", which is often cited by Touhou players as a reason to hate the randomness inherent in some cards; in Charming Siege, if the RNG decides it doesn't like you, you bomb or you die. Even if the RNG does like you, the card is still very hard, consisting of dodging between bubble bullets, almost invariably within their sprites. And these same bubble bullets tend to cover up the smaller pellets which attempt the entire time to wall you. Almost inexplicably, Yukari's version of the card in Phantasm is so much easier the card becomes a joke.
Another one that can ruin whole runs if the player is unprepared for it: Radiance "Princess Tenko-Illusion". Ran teleports throughout the card except when attacking with aimed bursts followed by a burst pattern making her immune to damage 2/3's of the time and being immune to bombs throughout the whole deal while the caster herself gets progressively faster slowly cutting off all routes of escape with increasing amounts of danmaku. Similar to Charming Siege, Yukari's version of Princess Tenko (here named "Yukari's Spiriting Away") is actually much easier, since the increase in bullet speed just means they clear the screen faster, not to mention how Yukari doesn't speed up herself.
Although Yukari doesn't share Ran's most dangerous attacks, she contributes her own: Double Death Butterfly. Butterfly bullets will start heading toward Yukari and then flying back down at incredibly awkward angles, and while they're flying down in ways that are nigh-impossible to predict, she'll be shooting dagger danmaku that flies straight down from all over the screen, which then proceeds to get pulled in just as the butterflies were - and with the Hitbox Dissonance associated with dagger danmaku.
And Boundary of Life and Death - it's the page image for Bullet Hell for a reason. The good news is that it doesn't get quite that hard until you get Yukari down to low health, but the problem is that having "only" four or five bullet types to contend with as opposed to the seven it eventually becomes can be more than overwhelming enough, and this card has a lot of health. At least Double Death Butterfly can be cheesed through if you bomb at exactly the right time thanks to the mechanics of the card - if there is one card during the fight that you will bomb multiple times over, it is Boundary of Life and Death.
Magic Sign - "Milky Way", used by Marisa. It fills the entire field with spirals of tricky-to-read star bullets, which then proceed to form smaller star bullets that hit you from the sides. Want to try and just slightly tap your way through the whole thing? Her familiars and their shotgun blasts laugh at you. And this is the first spell Marisa uses; thankfully the rest of the battle gets easier, though not by much.
There's also Apollo 13 from Eirin. It sprays huge amounts of bullets everywhere, and the pattern the bullets follow is ridiculously hard to make out. Even more obnoxiously, the bullets are immune to your bombs.
Fujiyama Volcano from Mokou, featuring bombs that take up large portions of the screen on top of extremely dense red circle patterns and extremely fast aimed streams.
And right before Fujiyama Volcano, we have the nonspell that has been given the Fan Nickname "rings of death". It moves at such an absolutely ridiculous speed, requiring superhuman reflexes even by Touhou standards, that losing two bombs to it is actually considered ideal; it's the second-fastest attack in the series only to Gengetsu's timeout phase. And since it's a nonspell, no Spell Practice for you. This video makes it look easy, but it's worth noting that the description specifically singles out the attack as essentially impossible.
Shoot the Bullet
When talking about impossible spell cards, nothing comes close to the photography game Shoot the Bullet (and by extension its sequel Double Spoiler), which is basically a collection of these. The game uses a unique control scheme, which makes beating spell cards as much an exercise in puzzle solving, as in bullet dodging. They start fairly easy, then get progressively harder, then reach the usual Touhou difficulty level, then pass it and then they keep going until they're completely Off The Scale.
Even by this standard, Kaguya's "Seamless Ceiling of Kinkaku-ji" manages to stand out, what with its circular spinning bullets, lasting for seven photographs and getting harder with each one. If you don't know how to properly herd the creation of the bullet streams, the card becomes even more impossible than it already is. It's vastly considered the single hardest card in the game, even though it appears in stage 9 out of 11.
Mountain of Faith
Nitori's spellcard as the midboss of stage 3 is pretty easy on Normal, but on higher difficulties, bright bullets are added that make the card almost a mandatory bomb; otherwise, prepare for extremely tight micrododging with a high probability of clipping.
Misayama Shrine Hunting Ritual, the 3rd spellcard from Mountain of Faith's final boss. Trying to navigate through knives aimed ahead of you while avoiding a pattern of circle bullets has stopped many a perfect runner on Normal. Everything else in the fight on Normal is trivial, but Misayama is ridiculous no matter how much practice the player has. Only appears on Normal and Easy, thank god.
Meanwhile, Kanako's final spellcard, Mountain of Faith/Virtue of Wind God, is That One Attack on two difficulties. It's considered one of the hardest attacks in the series on Lunatic, where you will get assailed with wave after wave of amulet walls that are dense and come at various angles, require quick dodging through some tight spaces—and, of course, like all final spellcards, it takes a long time to defeat and bombs do nothing. However, it is also That One Attack on Easy, where the attack is slowed down a lot; instead of making the attack any easier, it just clutters the screen with amulets and forces you to guess at the amulets' hitbox and make tight dodges between them, a skill most Easy players probably do not have. In fact, this attack is considered easier on Normal, as shown in this video, which shows just how brutal the attack is on the supposedly easiest difficulty.
And Kanako's penultimate attack on Easy is similar; making the streams slower makes them ridiculously dense. If anything it's even harder than the above pattern.
"Green-Eyed Monster", Parsee Mizuhashi's midboss card in stage 2, is notorious for being a wake-up call attack; introducing Parsee as the game's resident Puzzle Boss while also establishing that the bosses in this game are much harder than normal. It's homing, which is a trait usually reserved for stage 5 or 6 bosses in Touhou games, and is more than likely to catch players off-guard.
Yuugi's final card Knock Out in Three Steps; while up to this point Yuugi has been just messing with you, this card is a taste of what Yuugi can really do, requiring extremely tight micrododging even by the standards of Subterranean Animism, a game centered on micrododging. It also has a degree of randomness to make it possible to get walled, and can easily net a cheap kill if the player is unaware of how it works.
Satori's patterns differ depending on the shot type chosen, so thankfully it is possible to avoid any attack she is using, but even so Double Death Butterfly has to be mentioned. Yes, it's that Double Death Butterfly, ripped directly from PCB Phantasm. Of all the cards that ZUN could have brought back, why the hell did he choose that one? And it doesn't help that ReimuA, the shot type that has to face it, is otherwise considered the best shot type in the game.
ReimuC players on the other hand have to deal with Tengu Macro Burst, another really nasty one, especially for players familiar with Aya's boss fight in Mountain of Faith. The card is taken from Scarlet Weather Rhapsody and is highly likely to mess with the player's expectations. Even if the player is prepared, the card is still a tough one, with arrowheads bouncing around off the walls all over the screen.
Orin in Stage 5 has two of them: "Cat's Walk" and "Needle Mountain of a Former Hell", both of which require very quick micrododging. In the former, the micrododging is done at incredibly awkward and randomized angles, while in the latter, the micrododging itself is straightforward but the wheels of spinning spirits certainly aren't (and it's pretty tight even if you know how to predict the wheels). You'd be hard-pressed to find a player who wouldn't consider at least one of these the hardest part by far of fighting Orin.
Koishi has Rorschach in Danmaku, which requires you to dodge circular waves of bullets on top of each other, which will usually overlap to make dodging them nigh-impossible. And having three waves coming at once - often with two more following quickly behind - is not unheard of. If you don't have bombs ready...good luck.
And if you can beat that, there's another That One Attack waiting for you, and this one's much worse: Genetics of the Subconscious. Take the circular wave patterns from Rorschach, and add movement throughout the screen making Koishi nigh-impossible to hit, which essentially forces the player to time out all of it - almost two minutes of it. And the way the bullets spawn is merciless - to be more precise, they can spawn inside your hitbox if you're too close to Koishi, and some of them spawn off the screen where your bombs won't affect them and where you can't see them - leading to cases like this. Combine all of that with the bomb immunity expected of a Bonus Boss and you have yourself one utter nightmare of a spellcard.
Undefined Fantastic Object
Ichirin's King Kraken Strike, which shakes the screen while dropping erratically moving bullets down. It also forces the player to stay at the very bottom of the screen.
Murasa's timeout card Sinker Ghost. If you don't know what you're doing, you will get walled. Over, and over, and over again. And it lasts for 45 seconds.
Most Valuable Vajra, also known as Vajra of Perfect Buddhism, Shou's spinning laser thing that is almost impossible to deplete the HP of in the time given.
While the pattern is pretty doable on Normal, Byakuren's second nonspell on Lunatic is notorious for its stream of multiple quick homing lasers amidst a dense pattern of small fireball bullets. Almost impossible unless you follow a very specific route, which brings it from almost impossible to ridiculously hard.
Nue's Undefined Darkness. See Princess Tenko-Illusion, in the Perfect Cherry Blossom section above? Imagine that, except that the bullets are now erratic and all over the place, and some of them are covered by dark clouds that make them invisible, which means planning your route is nigh-impossible. Far and away the hardest spellcard in the Nue fight.
Story Mode Utsuho Reiuji's Artificial Sun's Spot. She fires rings of mini-suns, one of which has a sunspot. If you dash through that one, the whole ring disappears. However, on Hard and above, the rings contain so many mini-suns that you will probably run out of spirit before you've grazed through the correct mini-sun and you will get juggled for over 4K damage. However, you can also break the rings by shooting the spotted sun. It's easier for Cirno, who has a move that reaches across the entire length of the screen, but it's still very hard to do right.
See the Seamless Ceiling of Kinkaku-ji example from the Shoot the Bullet section? ZUN, being a Trolling Creator, decided to bring it back for this game. And make it harder. (Mercifully, however, you only have to take 3 photographs this time.)
Fittingly, it's used by Satori Komeiji, whose main gimmick in Subterranean Animism was copying the most traumatic spell cards from the protagonist's past battles.
Score Desire Eater, Yoshika's last attack on Lunatic, is one of the most notoriously difficult cards to capture that Ten Desires has to offer, due to being forced to get close to Yoshika among a storm of kunai, then squeezing through a bunch of curving lasers, and repeating this multiple times over. How difficult is this card to capture? Getting it once in under 200 tries is considered an excellent capture rate. For most cards, a good capture rate is at least once in under ten.
"Tongling Yoshika", Seiga Kaku's second-last attack on Hard and Lunatic, consisting of curving lasers, large thunder orbs, and dagger danmaku. Shooting Yoshika results in her getting very close to your character while still shooting the curving lasers and thunder orbs that become extremely hard to dodge due to their proximity. And suffice it to say, not shooting Yoshika is absolutely not an option.
Miko's penultimate attack, Laser of Seventeen Articles/Honour the Avoidance of Defiance, is another example, due to the lasers shooting out ridiculous numbers of amulet seals. "Ridiculous numbers" meaning "so many that it's hard to see the lasers". You best hope is to pray you can make it to the largest gap between lasers before the next wave fires. Get caught between a pair of close lasers? Good luck. And god help you if you're using Youmu while going for card capture.
In Labyrinth of Touhou, there's Djinn Storm, which empties all party members' SP, including the SP of those in reserve.
Destroy Magic, which reduces the SP of all active characters to 0; in other words, Djinn Storm, but less annoying.
Another highly annoying move is Shadowstep, which deals almost no damage, but more than makes up for it with an ungodly high chance to paralyze your party members.
Curse of Vlad Tepes is an odd example; it's a self-buff that does wonders on Remilia's offensive stats, but also has a chance to poison her and always paralyzes unless you can raise the resistance. If the poison takes effect, that means she will continually take damage when nobody is taking a turn, and her own turn will never come around until the paralysis lifts. Meaning she'll probably be dead before you can take advantage of the buffs. Oh, and there's no way to resurrect people outside of the dungeon. If you have Meiling or any other character that can clear statuses, then this isn't a problem.
Just about every major boss has one of these. The Final Boss, for instance, has a move that increases every single one of her stats by 75%. If she decides to use it twice, even over-leveled tanks with maximized defense boosts are at risk of a One-Hit Kill. Other boss moves include Chen's Kimontonkou, which is the first attack buff in the game that has no drawbacks. It also has low cooldown, so she can use Flight Of Idaten at least twice before anyone else gets a turn, and with the increased strength, it's almost a One-Hit Kill.
Slash of Eternity, used by Youmu. If you think that defeating her ghost half first is a good idea, this attack should change your mind, for the horrendous damage it can do to your members. And she uses it instead of Present Life Slash, the less-damaging version only seen with her ghost half intact.
Rinnosuke's ability to change elemental forms, making what's already a Marathon Boss even more drawn-out. Not only that, his inactive forms actually regenerate HP.
Yuyuko in Koumajou Densetsu II has Resurrection Butterfly, one of the few attacks in the game that can insta-kill you. Plus there's a red butterfly that constantly seeks you out throughout the fight, and if it touches you, you're dead.
In Marine Benefit, there's the stage 3 boss Tsubame Minazuki's second card, Great Ocean of Stormy Weather. Enormous bullets fill the screen and start moving all over the place, attempting constantly to wall you...and unlike most enormous bullets in Touhou, these have almost a 1:1 hitbox-sprite ratio. While it can be brute-forced with pure memorization, the paths to take completely change from one difficulty level to the next. And on Lunatic, there is one point where the bullets force you into a space that is the size of your hitbox - even memorization can't save you.
The Eight Million Laughing Gods is a very unique survival card - it goes with the fifth stage boss' gimmick of giving the player a bubble to stay in, killing the player if they go outside of it. It then shuffles the bubble all around the screen, making it all but certain that the player will - and by its nature, it is nigh impossible to properly deathbomb the card, meaning it can burn through resources very, very quickly. This card has no bullets fired at all, and ironically it's the most dangerous card in this Bullet Hell.
Megumi Yaobi, the aforementioned fifth stage boss, makes a return as the stage six midboss with only one spellcard: Silent Siren. She swore revenge after you beat her in stage five, and by the gods, does this spellcard ever show it. This card forces you into a fairly narrow trail of bubbles, requiring nearly constant diagonal movement at a fast pace, while at the same time dodging bullets coming from all around the screen at every possible angle with a nearly unreadable pattern. And if that wasn't enough for you, Megumi is Genre Savvy enough to block your path with her own body, since in Touhou, the boss' sprite is as lethal as any bullet. The Lunatic version in particular, here named A Fantasy's Transience, is so absurd its difficulty borders on parody. The only known Challenge Gamer to take on this card on Lunatic has explicitly called it harder than the above-mentioned Virtue of Wind God, despite the latter lasting five times as long. Here is her video of it.
Kanpukugu, the extra stage boss, has differing spellcards depending on which character you are using, so it is possible to avoid any of her cards by simply picking a different character. Not that it helps much, as all three characters have to face a "Gathering Void" card.
Sanae's card, Gathering Void -Rainbow-, fires lines of colored bullets while having colored smoke rise from the bottom of the screen. The smoke makes the bullets impossible to see. You have to memorize the color of the smoke, memorize where the bullets of that color are, and make sure you're in a spot where they can't hit you, all while dodging all of the other colored bullets that you can see. Commence brain overload.
Marisa's card, Gathering Void -Black-, creates a black Fog of War effect all around the screen at the same time it spawns bullets all around Marisa. Did we mention these bullets are black? Did we mention these bullets move in a pattern reminiscent of Apollo 13, listed above in the Imperishable Night section?
Reimu's card, Gathering Void -White-, is generally considered the worst one, which is really saying something. Before the card names were translated, Gathering Void -White- was colloquially known as "the impossible spellcard", with its vibrating bullets moving in awkward patterns and walling the player constantly while getting harder to see with every second that goes by. Words can't properly describe this card - it really does have to be seen to be believed.