All three Donkey Kong Country games on the Super Nintendo 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.
EarthBound memorably has a vast array of copy protection mechanisms of surprising intricacy and thoroughness. 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 * 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 mechanism 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 MOTHER, dubbedEarthBound Zero by the fans, 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.
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.
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 NES 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 10NES chip was also used in the Super NES and Nintendo 64. However, the top-loading NES II omitted the lockout chips entirely, meaning that theoretically, a game made for the NES II may or may not be playable on the original NES.
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. The discs are recorded at the factory and read by the drive from outside to inside (unlike normal discs, which are read from inside to outside). Unusually, some LG DVD drives have the capability to read such discs. as they are simply DVDs recorded backwards. Unfortunately for Nintendo, Wii pirates either disregarded the physical aspects of the copy protection and instead decided to attack the console's firmware, which had quite a few holes, or simply stuck the disc inside an LG-manufactured DVD drive and ripped the ISO from there.
There is also a rumor that the Gamecube spins it's discs backwards to further circumvent hackers. A simple peek under the lid right after turning it off will show you that they do indeed spin the proper direction (clockwise), people believe it to this day.
Communication between Pokémon Black and White games 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 realizes it's a bootleg, the game plays as normal... save that Pokémon don't gain experience points.
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.
The Wii (as well as Wii Mode on the Wii U) will deny any Virtual Console games on an SD card that wasn't installed through the console itself.
While Nintendo 3DS emulators do not exist yet, Nintendo seems to have prepared for it in Pokemon Xand Y. Inkay evolved into Malamar at level 30... with the 3DS held upside down.