Cowboy BeBop at His Computer: For months prior to the official release of the game promotional materials referred to the Pokémon Marill as "Pikablu" likely due to its mouse-like appearance, the zig-zag tail that resembled Pikachu's lightning bolt tail and... well, the fact that it was blue. Marill was never officially referred to by this name at any point, not even during the planning stages. Despite this the misnaming was so prevalent that even Topps used it in the Pokémon: The First MovieTrading Cards.
Silver (the rival, not the game) is sometimes jokingly referred to as ???.
The three games are collectively referred to as GSC and the Metal Generation.
A scrapped fire starter, Honoguma, is sometimes jokingly called "Pikaflare", just like Marill is called "Pikablu", due to its resemblance to Pikachu.
The names of Kris (the female protagonist of Crystal) and Silver (the rival) have never been confirmed. Kris' name comes from the English box-art while Silver's came from using the same Theme Naming as Blue Oak.
God Never Said That: Marill is very frequently treated as a Pikaclone by the fandom. While the parallels are there, Game Freak has never officially promoted Marill's line in that capacity, and the association is a leftover from the old "Pikablu" rumors.
Serendipity Writes the Plot: The limited space of Game Boy Color cartridges is more than likely the reason that many buildings and dungeons in Kanto have been scaled down or became inaccessible due to various plot reasons in Kanto. For example, Cinnabar Island's volcano erupted and destroyed almost everything, Fuchsia City & Cerulean City's shared music was replaced with that of Celadon City and Viridian City, respectively, and most of Silph Co. isn't open to the public. HeartGold and SoulSilver restores most of the areas and their music, though Cinnabar Island is still destroyed and the Fuchsia City Safari Zone has been with replaced with the Pal Park.
The game was originally developed for the original Game Boy, with Super Game Boy compatibility in the same vein as Pokémon Red and Blue, and was slated for release at the end of 1997. However, the game ended up being delayed to 1999, allowing Game Freak to take advantage of the then-new Game Boy Color by making Gold & Silver a Game Boy-compatible GBC title; Super Game Boy compatibility did manage to remain, though this feature was excised from Crystal, which needed the extra VRAM of GBC-only cartridges to store new features such as the animated Pokémon sprites.
Forcing Crystal to boot up on an original Game Boy shows a somewhat functioning version of the game's intro and title screen ("somewhat" being the operative word; both the intro and title screen feature a number of graphical glitches due to certain sprites being programmed to be stored in areas of the Game Boy Color's greater VRAM that the Game Boy lacks). Force-booting the cartridge on a Super Game Boy additionally brings up the border for Gold and an orange-beige screen tint. Trying to play the game results in it crashing when it tries to load the overworld, however. Nevertheless, this appears to indicate that Game Boy compatibility was planned for Crystal, but was dropped when it turned out to be too much for the original handheld to, um, handle.
Similarly to the above, the Korean versions of Gold & Silver, which are Game Boy Color-exclusive can also be force-booted on a Game Boy, though things tend to go haywire as soon as you get past the title screen due to the GBC's extra VRAM being used to store the rather large Hangul alphabet. The game is still playable, however, albeit in a very garbled state with occasional crashes; this seems to indicate that, as with the case of Crystal, Game Boy compatibility was planned for the Korean Gold & Silver but was dropped due to the Hangul alphabet being too big to fit on a Game Boy-compatible cartridge.
In an early build of the game, the name of New Bark Town was going to be Silent Hills.
Each town and city in Johto has an alternate map in the games' ROM with different layouts than the the final product. There is also a map for a town or city located in the Lake of Rage, complete with its own Gym.
Updated maps for Cinnabar Island's Pokémon Lab are in the data (though they have no event data), indicating that the island was originally going to return unchanged.
There's an unused script for an encounter with a Level 40 Entei, implying that it (and possibly Raikou and Suicune) was originally intended to be found in a static spot instead of randomly roaming around Johto.
Pre-release material promised a skateboard item (separate from the bike) that would be allow access to new areas.
An image◊ from the magazine MicroGroup Game Review shows unused designs for 2 Pokémon; a turtle that resembles Tirtouga from Pokémon Black and White and what can only be described as a Hitmontop and Clefairy hybrid (with elements of the later Pokémon Spoink). It also shows that Tyranitar was going to be brown instead of green.
A string of text in the ROM suggests that the Honey Tree mechanic that debuts in Pokémon Diamond and Pearl was originally intended for these games.
Staryu and Starmie may have been originally intended to have genders, as Staryu has Egg Moves programmed for it and both are able to be taught Attract (a move that only works if the user and target have opposite genders) in these games only.
In an "Iwata Asks" interview, it was confirmed that Gold & Silver were intended to be the last installments in the series, as the developers felt that they were too much of a Tough Act to Follow.
The battle with Red was originally planned to pull data fromPokémon Red and Blue so that Red would use the Pokémon the player used completed the original game with. This proved too difficult to implement with the technology available at the time, so the default option of the three previous starters and the plot-relevant Pokémon were used instead.
There's leftover code that allowed the player to name their mother. What this would have served isn't known, but this leftover data may have been used for the catching tutorial (which is used by Dude). Naming your mother would show up in MOTHER 3 released several years later.
Very early info mentioned that Ethan had a brother three years his senior that gave him a hand-me-down computer that he likes to tinker with. In the final versions of Gold and Silver, Ethan is an only child, computers aren't important to the plot, and he has no known personality traits. Contrary to popular belief, the brother was not Red. Incorrect translations simply assumed it was Red.
Satoshi Tajiri mentioned several unused plot details in an early 1997 interview. He said that the story starts when the protagonist learns of a boy in Kanto who completed his Pokedex, implying that Red was an important character and that the story took place directly after the original games. Satoshi also implied that Giovanni would return, when in the final product he is absent and he didn't return until an event for the remake.
A 1997 playable Space World demo featured completely different starters (the above-mentioned ones), different Japanese names for the Pokemon, and a vastly different overworld. It also had the starting town as named "Silent Hills". Some of the name changes were: "Eleking" for Elekid, "Puko" for Harysen (Qwilfish), "Sunny" for Kimawari (Sunflora), "Painter" for Doble (Smeargle), "Yoroidor" for Airmd (Skarmory), "Buku" for Otachi (Sentret), and "Animon" for Unknown (Unown).
Game Freak posted a unused character design for Kris once. The screencap was small but details could be deciphered. Kris still had pigtails but they were styled differently and her hair seemed to be black, not blue.
There was originally going to be a location called "Haunted House", as evidenced by an unused location name in the Japanese ROM. The idea may have been revisited with the Old Chateau in Pokémon Diamond and Pearl, much like the Sweet Honey talked about above.