Chrono Trigger allowed you to play until you first traveled back in time, then if it detected you were playing a pirated copy, it stuck you in an eternal loop in the warp sequence. This is present in both, the Super NES and Nintendo DS versions, and doubles as an semi-effective anti-cheat measure, as it also triggers when inifinite HP/MP Game Genie or Pro Action Replay codes are present (users can sidestep the anti-cheat aspect by only activating the Game Genie or Action Replay after arriving at their desired time period, and disabling the cheat device temporarily before time travelling).
Devil Survivor 2 has an anti-piracy routine during the fight against Dubhe. Dubhe has Story-Driven Invulnerability and is totally invincible until a cutscene where Daichi hits it with a truck, slashing its HP and making it weak to just about everything. However, if a pirated copy of the game is played, the cutscene will not occur. And while the original objective of the mission is to escape from Dubhe, reaching the escape point triggers said cutscene... and nothing else. The game may as well just shut itself off there, because no progress can be made.
Although there are ROMs of the game that seem to have been able to by-pass this little protection measure and have the game play out like the real physical copy...
All three Donkey Kong Country games on the Super NES featured variants of this if a copy protection trigger was tripped on the cartridge. The first game simply showed a blue screen featuring a generic "copying is illegal" message, while the latter two displayed a message mentioning an irregularity in the game cartridge/warning that piracy is illegal using each sequel's respective Game Over screen. It is unknown if these error screens were emulated on the Wii Virtual Console versions and Wii U Virtual Console versions.
The Dragon Ball video game trilogy known as "Legacy of Goku" (And the spiritual sequel, GT: Transformation) had its form of copy protection wherein a message popped up at a certain point saying "this game cannot be played on this hardware" note or "For pleasure not pressure..." on European copies and wouldn't go away, should it detect that it isn't a legit copy (Although there are rumours of some retail copies having this problem as well). Unusually, the emulator VisualBoyAdvance decided to emulate this form of copy protection, making playing the games on that emulator extremely difficult.
The catch: it checks for the Save Type Data and RTC. If the Save Data Type or RTC setting does not match the information concealed further into the cart, it will instantly declare that it is a "pirated cart". Since Emulators allows one to change these setting, they would set to Auto, right? Auto either pulls the settings from the cart/ROM or from a database. If pulling from an outdated database or from the ROM, it would retrieve a false data, telling to use an invalid Save Type Data. A vba-over.ini can be used to automatically set the save type to the correct setting, ignoring the false data.
EarthBound memorably has a vast array of copy protection mechanisms of surprising intricacy, thoroughness, and cruelty. For its first layer, it has a checksum that could detect whether the game was running from a copied cartridge or being booted from a cartridge-copying device note Emulating the game does not set it off unless you're using a really shitty emulator.; if the mechanism did not check out, the game threw up an antipiracy warning screen at the beginning and did not play any further. If the protection was cracked, a checksum mechanismnote partly consisting of several Event Flagsburied deep in the normal gameplay code would detect the change, and the game spawned many more enemies than usual - some even in places they didn't belong! - in an attempt to discourage further playing. If the player persevered through this or cracked this second layer, however, an even nastier surprise awaited: the game would freeze and severely glitch after the first part of the Final Boss fight against Giygas... and when you reset, you would find all your saves deleted! These copy protection schemes also triggered sometimes on legit cartridges, likely due to wear and tear over time. Although unrelated to copy protection, the same wear and tear can cause the game to run entirely in black and white as well.
The English NES prototype of its predecessor, dubbedEarthBound Zero by the fans and eventually released as EarthBound Beginnings, also had similar copy protection, but it's more mundane and far less cruel in its implementation. Instead of making the game impossible and scrubbing your save games at the end, it runs a checksum at certain points to test whether the game is pirated; if it is determined it is, it stops the game and throws up a screen saying that the game is an unauthorized copy and will not continue, and bricks the ROM/cart. This measure was part of a major headache in getting the ROM to work properly when it was first discovered and dumped in 1998, and owners of the actual physical prototypes are understandably concerned that the condition of the prototypes may set it off anyway. This protection wasn't in the Japanese version, nor does it exist in MOTHER 1+2 which is built upon the prototype data.
Final Fantasy Crystal Chronicles: Ring of Fates detected pirated copies. This caused the game to end after a while, with a "Thanks for playing!" message, which certainly confused many pirates. Why not have a "Stop playing this game now, you dirty pirate!" message? This game was allowed as a demo in many stores. The same message would play in the demos. The method of the Copy Protection was that the game would have around a 30-45% chance of a random check to see if the game was a proper game... each time you changed rooms in the dungeons. The demos were only given a certain amount of game memory and that did not include the key to stop the Copy Protection from activating. This truly was a great AP due to the way it confused so many Pirates.
Ghost Trick made all the text blank if you use a flashcart.
On certain emulators, Hamtaro Ham-Ham Heartbreak would not go past the character-naming screen due to an onboard protection system.
The Legend of Zelda: Spirit Tracks had this when you got on the train if you were playing a pirated copy. The controls for it wouldn't show up, so you would end up crashing into another train over and over again in the tutorial section. This was later patched.
Mario & Luigi: Bowser's Inside Story locks up at the file select screen. That was quickly patched, though. It also had a couple, lesser known ones: The tutorial battle with Bowser will go on forever because Bowser won't attack and Toadsworth won't do a tutorial which is required to progress (even if you say no to his offer). A second one occurs with another tutorial battle with a Goombule which won't progress because Starlow won't do a tutorial.
Mega Man Battle Network: Operate Shooting Star, a remake of the first game, prevented you from editing your folder, and initiated a battle with three Mets, the weakest enemy in the game, with every single step you took while on the Internet.
Game manuals for Nintendo 3DS games include a lovely bit of text: "Important! Read the Nintendo 3DS operations manual before setup or use of your system. This product contains technical protection measures. Use of an unauthorized device or any unauthorized technical modification to your Nintendo 3DS system, will render this game and/or system unplayable." Yes, Nintendo is putting it right there in the manual that if you attempt to modify your 3DS, they will attempt to brick it via firmware updates. The catch? At least one method of delivering these updates cannot be disabled, and (in theory, at least) all firmware updates must be accepted by the 3DS. It may or may not be true.
The North American version of the Nintendo Entertainment System used a proprietary (and patented) lockout chip called the 10NES, which would reset the CPU if it did not detect a corresponding key chip on the game cartridge. Among other things, this allowed Nintendo to keep tight license control (and censorship) over developers attempting to publish games on the console, not just users attempting to make their own copies. Several companies discovered ways to beat the chip, such as piggybacking a chip from a licensed cartridge (Game Genie style) or using a voltage spike to knock out (bypass) the authentication circuit. Atari Tengen notably obtained the specs of the chip by (falsely) claiming they needed it for evidence in a legal case of their own, using that information to make a duplicate chip, their "Rabbit" chip. Nintendo promptly sued them in return, winning one of two counts of infringement, but later choosing to settle out of court.
The big kicker is that variants of the 10NES were also used in Europe, and due to the NES' history in Europe there are two different versions of the NES over there, and each version had its own (incompatible) 10NES chip. And yes, many Europeans were angry at the fact.
Similar chips was also used in the Super NES and Nintendo 64, although this time it is likely that all regions used the same chip (the chip only assures that the cartridge was manufactured by Nintendo themselves, and has nothing to do with Region Coding- given that breaking (or filing) off a pair of tabs at the back of a North American SNES' cartridge slot was all it took to get Japanese games running). However, the top-loading NES-101 omitted the lockout chips entirely, meaning that theoretically, a game made for the NES-101 may or may not be playable on the original NES-001.
The Nintendo Gamecube used a proprietary 8cm DVD based on the miniDVD. Both the Gamecube and Wii discs use a slight variant of the DVD sector-level encoding. Contrary to popular belief, Nintendo optical discs aren't spun backwards nor they are read outside-in. While they're mostly the same optical format as with conventional DVDs, the main difference lies in obfuscating data on the disc, the encryption method used (which also involves the burst cutting area) and the proprietary filesystem. Certain DVD-ROM drives manufactured by LG are able to read through the discs, but these are rare and thus not readily available, so methods such as using Wii homebrew tools are a more viable approach.
Communication between Pokémon Black and White games and their sequels involves an infrared beam ... which is built into the Game Card itself. So using a flashcart means no (convenient) local trading/battling with other players.note Local interactions are still possible, albeit only in the Union Room, which places a few restrictions on battling. Other features, such as quick Friend Code exchanges, become completely inaccessible. Official Nintendo-sponsored tournaments also require entrants to scan their infrared upon entry, which means only official copies are allowed.
If a copy of Black or White as well as Black 2 or White 2 realizes it's a bootleg, the game plays as normal... save that Pokémon don't gain experience points.
Pokémon FireRed and LeafGreen actually had something added by the pirates who dumped the ROM: showing the Aurora Ticket to the sailor in front of the S.S. Anne would have him tack on "By the way: If you like this game, buy it or die." to his usual spiel.
Hackers had a field day when it came to Shin Megami Tensei: Strange Journey. Any pirated copies of the game would erase any saved data upon restarting, as well as not including any random encounter enemies whatsoever. The "save data erasure" assumed that the game even saves correctly (notably, on a LOT of cards, the game automatically stops saving halfway and states "save failed", and then deletes the failed save data when you attempt to load it), which turned out to be the least of your issues when you realized that the "random encounters" are actually required to stand a remote chance of making it through one round of a boss battle (Tool Assisted Superplay notwithstanding). Not that anyone who playsthese gameshasn't figured that out before getting this one.
At a certain point in StarTropics, you are instructed to enter a three digit codenote 747, for those curious to allow Sub-C to track down Dr. Jones. The game instructs you to submerge the letter that Dr. Jones gave you to find this code without clarifying that the "letter" in question was in fact one of the Feelies that came with the game. This aspect is simulated and digitized in the Virtual Console port.
Super Mario All-Stars has a message that displays when it detects an unlicensed copy (of course, emulators are able to bypass this easily). It also tells you to refer to your Nintendo game instruction booklet on the off-chance that your copy is actually legit. This message is most likely also in the Wii port, but it's unknown how to make it show up.
Super Metroid also has a message that displays an unauthorized copy. It is possible that Game Genies could trigger these messages.
Teenage Mutant Ninja Turtles III: The Manhattan Project would make enemies tougher and the bosses invincible if the copyright code was modified.
The Wii (as well as Wii Mode on the Wii U) will reject any Virtual Console games on an SD card that wasn't installed through the console itself.
So does the DSi and 3DS, and this also applies to native games and apps on the SD card. This is because each game downloaded is immediately stamped (and probably encrypted) with the ID of the console that downloaded the game. Simply taking your SD card and putting it into another Wii will not work because the new console won't honor the game if the ID is different (or simply can't decrypt the game because the encryption key's different). However, doing a console transfer somehow and then putting in the SD card will allow the games on the SD card to be played on the new console- at the expense of the game no longer being playable on the old one.
In a similar vein, in order to prevent duping and other tricks, Pokémon X and Y, if played as a digital download instead of a using the physical SD card, will stamp the install with the ID of the system AND the ID of the card. If you copy the game install from the SD card to another one (say, a larger one), the game will start up normally, but will give an error stating that it will not load your previous save and that you have to start over.