Chrono Trigger allows you to play until you first travel back in time, then if it detects you're playing a pirated copy, it sticks 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 feature variants of this if a copy protection trigger is tripped on the cartridge. The first game simply shows a blue screen featuring a generic "copying is illegal" message, while the latter two display a message mentioning an irregularity in the game cartridge/warning that piracy is illegal using each sequel's respective Game Over screen.
The Dragon Ball video game trilogy known as "Legacy of Goku" (And the spiritual sequel, GT: Transformation) has its form of copy protection wherein a message pops up at a certain point saying "this game cannot be played on this hardware" and won'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). The emulator VisualBoyAdvance used to have problems with this form of copy protection, which made playing the games on that emulator rather difficult.
The problem: 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 emulator allow 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 will 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.
The Game Boy's anti-piracy protection system is an interesting example, being more of a passive system that relies more on their lawyers, akin to Sega's efforts on the Genesis, than on EarthBound-style failsafes meant to cruelly penalize those who pirated it. The Game Boy boot ROM (often erroneously referred to by gamers as the BIOS, despite being technically more of a secure boot loader of sorts) checks for the presence of the Nintendo logo on the cartridge ROM, and if it matches the one stored on the boot ROM, the game loads up. Pirates can get away with just ripping it off an existing game for their bootleg titles to run, but as the "Nintendo®" logo is a registered trademark, that would make them an easy target for litigation: copyright may not be easily enforceable in certain jurisdictions, but trademarks are, hence the motivation for the scheme. A workaround taking advantage of a flaw in the system exists, as the bootloader reads the logo twice: once to display it on the LCD screen (along with the iconic "ping" sound), and the other to check if the original logo is in the cartridge ROM at all, to which a proof of concept method of subverting it was submitted by Argonaut Games in a rather amusing way to get Nintendo's attention, which was a stark contrast to how the Big N infamously intimidated unlicensed developers during the NES days.
Needless to say, the dual-logo trick was eventually exploited by bootleg developers in Taiwan, presumably as a form of Plausible Deniability should they be sued for releasing a game without Nintendo's permission, in that no trademarks are visibly violated, but that would be moot once the ROM is disassembled and studied.
This has however been rendered pointless once the courts ruled in Accolade's favour in Sega v. Accolade, where Sega's trademark enforcement system was questioned as being monopolistic, and bypassing it by third parties on the grounds that it is for the purposes of lawful interoperability was ruled as fair use.
The Famicom Disk System's copy protection mechanism relied on a conceptually similar principle: the disks, which are nothing more than a semi-custom variant of Mitsumi's Quick Disk diskette format, had the wordmark "NINTENDO" molded at the bottom part of the disk, with the I and second N activating a switch that authenticated the games. As with the Game Boy, bootleggers can easily get away with duplicating the molds, but instead resort to Paper Thin Disguises obfuscating the Nintendo name somewhat to "NINFENDO", "NINTEN", "NINJENDO", "INTEND" or any variation thereof. Then again, it's just the matter of making the right indentations on the disk without the need to mold the Nintendo name or the aforementioned corruptions at all, making the protection scheme next to useless. In addition, third parties in Japan sold adapters for conventional Quick Disks to be converted to an FDS-compatible disk.
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 can 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 doesn't check out, the game throws up an antipiracy warning screen at the beginning and doesn't play any further. If the protection is cracked, a checksum mechanismnote partly consisting of several Event Flagsburied deep in the normal gameplay code will detect the change, and the game spawns many more enemies than usual - some even in places they don't belong! - in an attempt to discourage further playing. If the player perseveres through this or cracks this second layer, however, an even nastier surprise awaits: the game will freeze and severely glitch after the first part of the Final Boss fight against Giygas... and when you reset, you'll find all your saves deleted! These copy protection schemes also trigger 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, has 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 freezes the game and throws up a screen saying that the game is an unauthorized copy and will not continue. 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 detects pirated copies. This causes 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, and this same message would play in the demos. The method of the Copy Protection is that the game has around a 30-45% chance of a random check to see if the game is a proper game... each time you change rooms in the dungeons. The demos were only given a certain amount of game memory and that does not include the key to stop the Copy Protection from activating. This truly is a great AP due to the way it confused so many Pirates.
Ghost Trick makes all the text blank if you use a flashcart.
On certain emulators, Hamtaro Ham-Ham Heartbreak will not go past the character-naming screen due to an onboard protection system.
The Legend of Zelda: Spirit Tracks has this when you get on the train if you're playing a pirated copy. The controls for it won't show up, so you'll 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 has a couple of 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, prevents you from editing your folder and initiates a battle with three Mettaurs, the weakest enemy in the game, with every single step you take while on the Internet.
If Mega Man Battle Network 6 detects that the copy of the game is not legitimate, MegaMan will interrupt the game in a text box to say the game is defective and you should buy a real copy of the game, then refuse to continue any further as the text box cannot be exited.
Mega Man Battle Network 4 has a glaring problem that ultimately makes the game essentially unplayable without serious perseverance or an emulator. During the WoodMan event, should the player jack in to the net and fight an enemy, the player will find the music still playing to a totally black screen. Waiting a couple minutes will reveal the game is not frozen, but rather running somewhere around 1 frame per 30 seconds, essentially making navigating the entirety of the net to reach WoodMan fundamentally impossible without a lot of patience. Regular battles will perform normally, and the game runs properly after the event is over, but the event will always trigger this effect because of one thing: the cartridge scans to see if it's being played on a standard GameBoy Advance and only the standard GameBoy Advance. If, at any point, you put the game in a GameBoy Advance SP or a Nintendo DS and turn it on, the game will flag the cartridge and cause the anti-piracy to activate. This is present both on the Red Sun and Blue Moon versions, but can only be triggered on the Red Sun version if a Blue Moon player swapped data with a Red Sun player as the WoodMan event is version exclusive until doing so. Thus, not only are Blue Moon players essentially screwed, but Red Sun players will be accidentally screwed by their own friends/their own cartridges when doing this.
This wouldn't be a huge problem if Red Sun had all of the same content as Blue Moon. However, certain battles, such as ProtoMan or the previously mentioned WoodMan, are version exclusive, and some, like Roll and ProtoMan, are locked to New Game+, so Blue Moon players can't even face every boss before the game breaks down, and Red Sun players have to accept that certain bosses cannot be fought at all for risk of triggering the anti-piracy.
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 ultimately turned out to be an empty threat.
The North American version of the Nintendo Entertainment System used a proprietary (and patented) lockout chip called the 10NES, which 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, each with its own (incompatible) 10NES chip. And yes, many Europeans were angry at the fact.
Similar chips were also used in the Super NES and Nintendo 64, although this time it is likely that all regions use 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 is all it takes 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 Gamecube and Wii discs use a slight variant of the DVD sector-level encoding, making it more or less a DVD-like optical disc format with Serial Numbers Filed Off. 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 of the era also required entrants to scan their infrared upon entry, which means only official copies were 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.
If Pokémon HeartGold and SoulSilver detects it's being played on a flash card or emulator, the game will freeze and the player's Poké Balls will spin forever at the start of a battle.
Pokémon FireRed and LeafGreen actually have something added by the pirates who dumped the ROM: showing the Aurora Ticket to the sailor in front of any one of the Seagallop ferries 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 will erase any saved data upon restarting, as well as not including any random encounter enemies whatsoever. The "save data erasure" assumes 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 realize that the "random encounters" are actually required to stand a remote chance of making it through one round of a boss battle (Tool Assisted Superplays 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 is in fact one of the Feelies that came with the game. This aspect is simulated and digitized in the Virtual Console port.
The Wii (as well as Wii Mode on the Wii U) will reject any Virtual Console games on an SD card that weren't installed through the console itself. So do 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.
The Professor Layton series has a tradition of using bonus material for their games. In order to ensure that you get the content, they include a password from a previous game that can be used in the oncoming one. The catch is that the password you get corresponds to your own game system, so if you're trying to get content with a password from a friend's game system or from a site, you won't get anything.