From Bulbapedia, the community-driven Pokémon encyclopedia.
ROM hacks, also known as fangames or bootlegs depending on the circumstances, are video games that have been edited or altered. While many honest fans distribute hacks of Pokémon games for free over the internet, some unscrupulous people have been known to sell them in the guise of legitimate games. Some of these games are hacked onto the actual game cartridges and sold over the internet on sites such as eBay. There are an uncountable number of hacks available on the Internet (a search on YouTube will easily reveal at least a dozen), so this article will limit itself to only the most notable ones.
It should also be noted that all current Chinese language Pokémon game cartridges are pirated as there have yet to be any official Chinese language Pokémon games.
Moemon (short for "Moekko Monsters") is another hack of Pokémon FireRed that changes all Pokémon into gijinka. It is a simple change of FireRed, but with additions such as the ability to catch the three starters, Eevee, and a mix of both LeafGreen and FireRed Pokémon (thus making it simpler to obtain all Pokémon).
Moemon received a short burst of fame when it was posted to gaming site Kotaku in late 2007.
Pokémon Adventure is a hack of an existing pirated game called Sonic Adventure 7 that is for the Game Boy Color. It has five levels, and the intro sequence consists of a few Japanese Pokédex screenshots from Gold and Silver. Other than the intro, title screen, and ending, the game has almost no relationship with Pokémon, with most of the enemies being from other pirates made by the same company, such as Rockman 8 and Super Mario Special 3.
Another infamous hack is Pokémon ChaosBlack, which is a modification of Pokémon FireRed that was released on the Game Boy Advance. This game contains many fake Pokémon, including Mewthree. Although it has a reputation as a bootleg cartridge sold illegally, the original creator of the hack released the patch for it onto the Internet. ChaosBlack is infamous for including numerous created Pokémon and harsh language.
The description on the back of some boxes can inform gamers that it is a bootleg, as there is a missing accent on the "e" in "Pokémon". Another large giveaway is the fact that Chaos from Sonic the Hedgehog games exists on the front cover. Also the game was apparantly developed by 'Mewthree Inc.' instead of Nintendo, meaning it couldn't have been endorsed by Nintendo, Pokémon's usual trademark. Despite these obvious flaws, the bootleggers still included a fake Nintendo Seal of Approval on the box and cartridge.
Pokémon Diamond and Jade
Possibly the most well-known bootleg "Pokémon" games are the notorious Pokémon Diamond and Jade (not to be confused with the official Generation IV games Diamond and Pearl). In truth, these games were poorly translated versions of a Japanese game known as Keitai Denjū Telefang. Telefang was divided into two versions: Power and Speed; the Power Version became Pokémon Diamond and the Speed Version became Pokémon Jade. Pokémon Jade was sometimes released on the Game Boy Color on the same cartridge as Pokémon Crystal, but could also be found as a standalone cartridge. The hacks had numerous glitches that the original game did not have, such as the inability to load a save properly. The game also contains profanity and swearing, which is absent from all official Pokémon games licensed by Nintendo.
Pokémon Diamond 2 and Jade 2
Similar to the first fake Diamond and Jade games, Diamond 2 and Jade 2 were hacked from Keitai Denjū Telefang 2. Also, like Diamond and Jade, the Power Version of Telefang 2 became Pokémon Diamond 2, and the Speed Version became Pokémon Jade 2. They are in Chinese, and their title screens have been altered to poorly drawn Pokémon characters. The similarities between the title screens of this and the original Diamond and Jade (as well as the fact that they have Pokémon names in the first place) suggest that these may be made by the same pirates. Diamond 2 crashes after the title screen, making it unplayable without a save state, and Jade 2 has graphical glitches. There is also a poorly translated English version of the Power Version of Telefang 2 called "Pokémon Ruby," which has no relation to the real one.
Pokémon Naranja is a hack of Pokémon Ruby in which the player plays as either Ash or Misty and travels around the Orange Archipelago. Naranja is a Spanish word which means Orange. Strangely, "naranja" is Spanish for the fruit orange, while "anaranjado" is Spanish for the color orange. This could be because many of the places in the Orange Archipelago are named after fruits. Celebi appears on the box art and title screen.
This game is based on the Orange Saga in the anime. The game starts after the player had won the Indigo League. Despite this fact, the player starts with only a Lv. 5 Pikachu. Many characters, plots and events in the Orange Saga are included in the game, such as the GS Ball, Ash's Lapras, the Orange Crew, the Crystal Onix, the Golduck from Bye Bye Psyduck, and Ash's Snorlax.
This game also includes a special feature: the player's character actually speaks during some of the story sequences, which has never been implemented in any official Pokémon game.
The game maker originally planned to release a third beta version before Christmas in 2005; however, the creator canceled this for an unknown reason. Therefore, the game is currently incomplete.
Naranja has, much like Chaos Black and Shiny Gold, also been published in cartridge form and sold as a bootleg game by pirates.
Pokémon Brown's title screen
Pokémon Brown is a hack of Pokémon Red. This hack began production in mid 2002, as a sequel to Koolboyman's "Rated M" ROM hack "Fukemon", titled "Fukemon 2". Finally, on January 16th, 2004, the hack was released to the public. The hack has a complete change of all maps and has some minor script tweaks. Also, almost all the Pokémon sprites have been changed. Pokémon Brown takes place in the Rijon region. The maker of this hack announced a remake of Pokémon Brown that was released in April 2009. The remake contains second and fourth generation Pokémon, new areas, and new additions to the storyline.
Pokémon Prism is a hack of Pokémon Gold made by Koolboyman, as another entry into his series of hacks, preceded by Pokémon Brown. This hack completely overhauls the original game, and also won Pokécommunity's Hack of the Year award in 2007.  It takes place in a new region called Naljo, with new music, new Pokémon types, and more. One feature is to replace the player's sprite with another at a special shop. The game also has crafting systems (not fully implemented as of the second beta release) and the ability to send a Pokémon out of its Poké Ball outside of battle. Like many other hacks, Prism is still in progress, with periodic updates being released to the public.
Another hack of Pokémon Ruby, released by the author as a patch file intended to be played by VBA users who already owned the Ruby cartridge and had a copy of its ROM image. The game has a great number of spelling and grammatical errors, which result from the hack being translated from Spanish, although the grammar improves throughout the game. The game also contains profanity and adult themes, which are absent from all official Pokémon games. Pokémon Quartz replaced all names and graphics of traditional Pokémon with new, made-up Pokémon, although some of the changes were only cosmetic and did not change learnsets or types. The game takes place in a region known as "Corna", a heavily edited version of Hoenn, and requires the player to navigate a very different series of paths during gameplay.
While the best-known bootleg cartridge as played on the actual GBA contains serious glitches and errors, the current patch file release works well with VBA when the patch is applied to a clean image of an actual Ruby cartridge.
Zorak of Something Awful did a complete Let's Play playthrough of the game, which ended in an interview with the creator of the hack.
A sequel to the game, Pokémon Marble, is in its beta release. This version is a hack of Fire Red and has vastly improved grammar and spelling.
Screenshot from ShinyGold
Pokémon ShinyGold is a total conversion of Pokémon FireRed that turns the game into a Gold and Silver remake, much like how FireRed is a remake of Pokémon Red. It is considered by many people to be among the best and one of the highest-quality hacked games. As well as illegally releasing the game to ROM communities as a patch, some pirates have copied the hack (as with many others) to Game Boy Advance cartridges to illegally sell the game and trick gamers who genuinely think that it is an official Pokémon game. In response to this, Zel (the creator of the hack) placed a note at the beginning of the game saying that the game should be returned if the player paid for it. The game features changes to allow Pokémon that normally evolve via time-based events or trade to evolve by other methods that are more easily available to the player. For example, Scyther evolves into Scizor with a Moon Stone rather than by its normal method, trading while holding a Metal Coat. The game also features many events which were not available in the original game, as well as many Generation III Pokémon being found in some areas.