Fist of the North Star has the sacred martial art, Hokuto Shinken, which apparently comes with a specific technique for violently countering any attack as well as inducing Karmic Death in any manner of villain (for example, if you garrotte people to death because you're evil, the right combination of pressure points will cause you to decapitate yourself with it). In an interesting example of characterization involving this trope, the later volumes see the main character relying less on cute special techniques to kill random Mooks and being content to merely punch them into pudding (unleashing your hidden brute strength is another of the style's techniques...)
Mazinger Z: In one episode, an enemy was unceasingly shooting missiles at the Hover Pilder to preventing Kouji from docking with Mazinger. Kouji pressed a button, and his vehicle let go a trail of smoke to make the enemy believing he had been shot down and having him stopping to shoot as he docked.
Juzo Kabuto from Shin Mazinger is a very well-prepared Mad Scientist. In addition to building escape routes all over the city, he also created a secret Shinto command center inside a shrine, complete with 100 armed Bodhisattva statues projecting images from their eyes and operating dozens of levers and switches at once. The shrine functioned as a remote control for the series title Humongous Mecha, in case his grandson found himself unable to pilot. Tsubasa even more so, with enough firepower at her inn to let four badass men and one woman hold off legions of robots single-handedly.
Urusei Yatsura: Lum nearly always carries around some kid of weird alien device is useful to the situation at hand (and usually it makes the trouble one hundred times worse). It is also lampshaded: during one Christmas party in Shutaro's manor, Ryoko -Shutaro's little sister- has planted several dozen of bombs around the place (in revenge for not getting invited to the party by her brother). Lum says she has an explosive detector, and Ataru asks if she always carries one around.
In Elfen Lied, Bando spends every day picking up trash from the beach so it can't be used as a weapon against him.
We are told that Hayate the Combat Butler keeps multiple flavors of jam packets in his pockets. Nagi also mentions that when a master asks for gum, any properly trained butler will have EVERY possible flavor on hand... just in case.
In an episode of Demashita! Powerpuff Girls Z, Miss Keane has a counter on hand for any bizarre excuse the girls come up with to leave class, thinking they're trying to cut class. These excuses include a hip ulcer, having to go into space, and attending a wedding of mole people. She also calls the President of the USA, and is nearly able to charm Mojo out of a rampage.
Mayuri Kurotsuchi invoked this trope in his fight with Szayel Aporo Granz, revealing a crazy number of preparations. To whit, he:
Planted bacteria on Ishida during their previous fight so he could monitor him.
Made it so his Bankai could self-destruct if it was ever used against him.
Replaced all of his organs with fake ones to render himself immune to Szayel's voodoo-style powers.
Planted poison in his vice-captain Nemu's body in case she was subject to Body Horror.
All of the preparations he made prior to arriving wound up getting used, even the ones that Mayuri couldn't have planned for based on what he had seen of Szayel's abilities thus far (like his ability to infect and control other beings, or his squicky method of resurrection). This led to jokes in the fandom about how Mayuri had reached "Batman levels" of planning. Going even further, in one of The Movies it's revealed that he keeps a backup brain with a copy of all his memories.
There's even an aversion with Mayuri. It turned out Mayuri was the one person who predicted the invasion of the Vandenreich all the way back in the Soul Society arc. The sole reason the Gotei 13 was not prepared for the invasion was because Mayuri's request to start planning like mad for just such a scenario was dismissed as too crazy and paranoid by Yamamoto. As a result, Mayuri was banned from being allowed to be this trope and had to settle for being The Cassandra instead.
Ichigo explodes out of the garganta and swings his sword at the back of Aizen's neck. He gets blocked, not because Aizen saw him coming, but because he has a shield on the back of his neck.
The whole plotline of Bleach is viewed by the fandom as one long crazy prepared chess game between Aizen and Urahara. In fact, Mayuri himself wouldn't be able to have achieved all his cazy prepared examples without Urahara's own planning that secured Mayuri's release from prison and take-over of the 12th division and Research and Development Institute that has allowed him the opportunity, time and resources to engage in crazy preparation. It has been lampshaded in the story when it was pointed out that Aizen creates the worst-case scenario outcome while Urahara counters it with a best-case scenario solution to that worst-case scenario outcome. It's even been observed in-universe that over a span of one hundred years, Urahara has made no miscalculation.
In the Houshin Engi manga, before the battle between the Yin and Zhou, Taikoubou gives the commander of the Zhou army a manual containing every possible move the Yin army could make and how to counter it. He made it the previous day.
Shikamaru Nara, Naruto's version of Batman, has been shown in the anime thinking of plans and strategies to use against various Akatsuki members if he were to fight them. Later he preplanned a fight against two supposedly immortal Akatsuki. Guess who came out on top? Subverted when he fought Temari and thought of nearlly 100 plans in his head—none of which would have worked because of his own physical lacking. He's since largelysurpassed these limitations.
The Fourth Hokage deserves an honorable mention here as well after the events of issue 439, where it is revealed he built a fail safe into Naruto's seal so he would appear if Naruto ever lost control in order to restore order.
In Chapter 370, it's indicated that he may have sealed the Nine-Tailed Fox into Naruto as some sort of preparation against Madara Uchiha, and sealed the Yang half of the fox's chakra into Naruto in order to have him one day complete a jutsu that would enable him to control the fox's power.
Chapter 498 it is revealed he also put Kushina into the seal, to appear to help Naruto gain control of the Kyuubi. Later on it is also revealed he put his own personal teleportation seal into Kushina's seal, so that he could go to her whenever he wanted.
Itachi Uchiha also deserves honorable mention for having two contingency plans set up to ultimately protect Sasuke. They both failed completely, leaving Itachi with his backup plan of "Wait for Naruto to fix everything"
In his final battle, Kisame demonstrated this trait. After preparing a scroll containing vital intel, he was found out by enemies and attempted to flee. Knowing he couldn't escape, he summoned a shark to carry the message, only to be intercepted. So he summoned a few hundred spares to distract the enemy before personally launching a massive attack. When all of that failed and he was captured, he had his own summons kill him, ending the threat... until his intel scroll turned out to be a trap that held his enemies still while a new shark summon made a run for it with the intel!
For her final battle with Madara Konan prepared six hundred billion exploding tags.
Movie villain Dotō Kazahana has a train equipped with kunai gatling guns, a blimp and a suit of armour that has functioning wings, which says a lot about him considering the level of military technology in the rest of the world.
Light Yagami of Death Note. One of the most astounding examples is his decision to hide a miniature TV within a packet of potato chips (a flavor the rest of his family hates) in case of surveillance cameras being placed in his house, so that he can use the TV to gain information on criminals without it showing up on camera.
He also schedules killing of criminals in advance, so that in case he falls sick and lands up in hospital for weeks, he would not be suspected of being Kira.
The TV was only a tactic devised as a result of an even moreCrazy-Prepared plan he had to test if anyone went in his room without him knowing; 1) tilting the door handle down slightly in the closed position; if people return it to the normal closed position after leaving the room, he will notice that they went in 2) lodging a piece of paper in the door that would fall out if it was opened and 3) having expected and intended the people who wanted to sneak into his room to find and replace the paper, putting pencil lead that would break if the door was opened onto the door hinge. There's also his creating the hidden compartment in his desk drawer with the igniting gasoline trap to prevent anyone from finding the Death Note itself.
In a subversion of Chekhov's Gun, the hidden compartment is never triggered. It's just to establish that Light is, in fact, Crazy Prepared.
L, under 3 different aliases, has made sure he's the top 3 detectives in the world in case somebody wants to learn his identity. This is just a small example, because to try and list every single Crazy-Prepared thing he's done would just be impossible.
What takes the cake for L being Crazy-Prepared comes from the live-action film series, in which he writes his own name in the Death Note just in case Kira decided to do it, setting his date of death at a certain time in the future and couldn't be altered. While this might seem more "crazy" than "prepared" this is what lets him catch Light, which is something his anime and manga counterparts failed at.
When you take into account that he had previously met Mello, and therefore chosen Near as his successor, it gets insane when it appears he expected Mello to go off on a race to solve the case (Rhyme not intended,) and therefore deliberately set up the duel of detectives in the second half of the story for the sole purpose of uncovering whoever had killed him. In other words, the whole ending was L's plan, which explains why Light had the constant feeling of facing L throughout.
One seriously overlooked item in the End Of Evangelion is when the Geofront rises out of the ground. Apparently, in addition to their Everything Sensor, Nerv has an altimeter on a stationary geological feature. Not only do they know and say what their altitude is, but it's in BOLD in a corner as if it's been there all along.
Yu-Gi-Oh! and all of the card playing characters use this trope to the extreme, with characters countering, counter-countering and counter-counter-countering each other regularly and with ease.
Lampshaded in the the Abridged Series quite a lot. "I play this card, which would be completely useless in any other situation!"
Happens in the real life version of the game much more than one would expect; or maybe not, seeing how counters and traps and effects that work against each other are the whole point of the game. For example, there's a counter trap called "Counter Counter" which specifically counters the use of any other counter trap, which are only used in response to something else, up to and including trap activation. So, theoretically, you could use this to counter your enemy's attempt to counter your counter to a spell of theirs.
Subverted in the case of Kodo Kinomiya from Yu-Gi-Oh! 5Ds. His plan in the Fortune Cup was a lot like that of Daichi Misawa's: Use a deck designed with that of his opponent's in mind. However, Aki had at least one card that he did not even know about, and was not prepared for at all, and it caused him to lose... painfully. (In fact, one might say that he was hardly prepared at all, and might fall into the Stupid Evil spectrum; he was confronting a woman with powerful Reality Warping powers and a very bad temper, and spent the whole duel insulting her?)
Inori Yamabuki. Whoever brings an umbrella to the amusement park to protect from splashing water caused by log flume?
In Baccano!, it's shown that the Daily Days newspaper company has seen to it that every single employee in their headquarters keeps a loaded gun in or under their desk, which they're instructed to take out at the slightest suspicion. It's taken even further in the novels, where desks and supplies are carefully arranged so that, should a firefight break out, all employees have access to cover while intruders are wide-open and thoroughly screwed.
Sagara Sōsuke from Full Metal Panic. He has, at hand, any and every kind of weapon you can possibly find. And he can pull any of them out at any time from... somewhere. In one episode he's shown to even have a biochemical suit handy, which he promptly puts on. He received by error a biochemical weapon, so he must have "somehow" prepared it in advance.
Kiritsugu Emiya from Fate Zero. Having been bound to a contract not to perform an actual murder, his associate barges into the hostage situation with a machine gun.
Kirei Kotomine with his bulletproof priest's robes.
In Mahou Sensei Negima!, Negi's ability to be Crazy-Prepared is pointed out as his greatest strength. This is seen most clearly in his fight with Jack Rakan. The kid essentially learned an anti-army spell, completed several techniques that his master had given up on after hundreds of years of work (which he combined with said anti-army spell), and created his own uberspell from scratch...to use as a distraction, so he could set up his real plan. Upon that failing, he reveals that he was still delaying one high level spell "Just in case".
Mana has shades of this as well.
Yue takes the cake, having embedded a time-delayed anti-paralysis spell into herself as a guard against one her "sixteen predictions". She was right.
As does Chao Lingshen.
In Combattler V, an episode involves the villain kidnapping the team's super scientist. He then exploits Professor Yotsuya's drinking problem to make him drink some wine with truth serum in it. Luckily, the professor had a capsule with an antidote hidden in his teeth.
In an episode of Outlaw Star set on a space station where conventional firearms are forbidden due to safety concerns, Gene Starwind for some reason has paintball bullets for his gun which he uses to disable the visual sensors of a Powered ArmorMini Mecha.
Fridge Brilliance! That tactic would work pretty well on damn near anyone, making them a sensible alternative. He probably replaced all his ammo the instant he learned about that policy - the instant you take guns off the table, you're catnip to the next psycho with an axewho will know for certain that you're not armed, let alone over-funded pirates with Mini Mecha.
Ah Blue from Pokémon Special. When exactly did she think to stuff her shirt with Pokeballs and pretend her Ditto is her arm before her actual battles? She screwed her opponents good. She also always takes careful notes on everything she does, which backfires on her when Silver steals them to figure out where the final battle would take place despite the fact she didn't want him anywhere near it.
Giovanni also shows shades of this as he always brings a Mewtwo Restraining Bolt on him just in case the Pokemon unexpectedly shows up to try to kill him.
The Team Rocket trio in the Best Wishes arc of the Pokémon anime. As a result of them taking a level in Badass, rather than being blasted off again by Ash and Co. (especially Pikachu), they now blast themselves off with jetpacks before the heroes can even deliver the finishing blow on them.
Armbrust from Kiddy Grade never traveled without his metal case. The case (called the Black Box) has extradimensional powers and can shapeshift, enabling him to transport things, people, anything the situation may demand, and he always seems to show up just when he's needed. The case is also bulletproof, and can repair damage at the press of a button.
When Reiko, one of the Gate Keepers whose power of illusion is activated through her piano playing, ran away with the Gate Robot, Invaders suddenly attack! It's a good thing the Gate Keepers' secret agency A.E.G.I.S. just so happened to have a secret weapon for the Gate Robot: GR 05 V, which was essentially a giant piano.
He was prepared for every possible setback against the Straw Hats. After imprisoning the Straw Hats, he tosses the key into the mouth of a crocodile in a whole pack of crocodiles (making it difficult to figure out which one ate the key) and explodes his underground base, so that the Straw Hats would drown. When it looked like the Straw Hats found the right crocodile, Crocodile reveals that key was a fake and he had the right one on him the whole time. In fact, if it wasn't for him not knowing about Sanji and Chopper and Mr 3 managing to survive inside a crocodile, the Straw Hats would have been dead.
There was also his plan with the bomb in Alabasta. He engineered it so that even if the cannoneers are defeated, the bomb was rigged with a timer. And when forced to fight with his hook, he has a poisoned backup hook underneath that hook. And if that hook is broken, he can eject a knife in its place.
How does one defeat a phoenix, a being who's immortal, in High School D×D? Simple; have a Longinus that doubles your power every 10 seconds, have a cross and holy water in handy, a skill that enhances the effects of anything you desire, and sacrifice your arm to turn it into a dragon just so you don't get burned by the effects of the cross and the holy water. Oh and as a backup, have two bottles of holy water in handy. This is what Issei did to finish off Raiser.
Shiro from Adekan certainly counts. While he doesn't have a different skill or object for every possible occasion, most of the trouble he encounters is easily solved with sharp weaponry, and he carries roughly 10 or 20 knives on his body at all times.