Pokemon Gold, Silver, and Crystal were the first Pokemon games to consider the use of a real-time clock and calendar as to be able to vary the catching possibilities of Pokemon based on time of day. While every Pokemon game since has used such a time system, it wasn't until the release of Pokemon Diamond/Pearl that the graphics again changed to be darker at night, for example, or that the actual day was considered.
As you probably know, the Safari Zone is not actually in Pokemon Gold, Silver, and Crystal, even though (outside of these games) it was a mainstay of the main Pokemon series through HeartGold/SoulSilver. In reality, a Safari Zone was indeed planned for G/S/C: however, it was taken out at the last second. The data for the Safari Zone's geography and wild encounters still remain in the game, however: if you use walk-through-walls cheat codes, you can even find the well-hidden "doorway" to it!
One of the Pokemon introduced within this generation, Blissey, has the highest possible HP of all Pokemon - not just highest of all Pokemon, but the highest by the limits the game sets. Blissey will have a base of 255 HP, which translates to 714 HP assuming max EVs and IVs in HP. Before G/S/C was released, Blissey's evolutionary predecessor in Chansey had the highest with 250 base HP (704 HP at best). Additionally, even as of the release of Pokemon X/Y in 2013, Blissey and Chansey give out the most and second-most EXP., respectively.
One of the Pokemon introduced within this generation, Shuckle, has the highest Defense and Special Defense stats among all Pokemon (as of Pokemon X/Y's 2013 release at least): a base of 230 in each stat, which translates to a whopping 559 points in either stat with maximum EVs and IVs. This is why Shuckle is commonly used as a tank in general competitive gameplay.
When it comes to the cumulative value of all of a Pokemon's stats, most people would jump to Magikarp as being the weakest Pokemon. However, the weakest Pokemon by base stat total is Sunkern (a new Pokemon introduced with these games), whose base stats total only to 180, whereas Magikarp's total to 200: the other Pokemon below Magikarp include Weedle and Caterpie, as far as those available in Pokemon Gold/Silver/Crystal are concerned. These numbers still stand accurate as of the release of Pokemon X/Y in 2013.
In the GameBoy Pokemon games, a Pokemon would have five stats: HP, Attack, Defense, Special, and Speed. Pokemon Gold and Silver introduced a sixth stat, Special Defense (Sp. Def.) while renaming Special to Sp. Atk. Back in the GameBoy Pokemon games, Special would serve as the role of both Sp. Atk. and Sp. Def., meaning your Special-class attacks' damage input AND output were determined by one stat, creating a painful imbalance in some cases that the stat separation remedied.
Pokemon Gold, Silver, and Crystal are the first Pokemon games in which Pokemon can hold items for their use in battle. This is evidenced as early as the start of the game where your starter will be holding a Berry (equivalent to the modern Oran Berry).
Pokemon Gold and Silver were the first incidences of Shiny Pokemon in the Pokemon series: Shiny Pokemon are those whose sprites are different than normal, such as a red Gyarados rather than blue. The odds of finding them are about 1 in 8,192 (until the 2013 release of Pokemon X/Y). Finding Shiny Pokemon in Gold/Silver/Crystal was also more unusual than the other games; every Pokemon has a set of "IVs" in each of their stats that helps to determine stat growth. In Pokemon G/S/C only, a certain specific set of IVs would determine Shininess - after that, it was simply a shot against the RNG.
Pokemon Gold and Silver introduced two new Pokemon types in addition to the fifteen previously present: now Pokemon could also be Dark- and Steel-types. This had an effect on some of the Pokemon already present: for example, Magnemite changed from Electric to Steel/Electric.
The music theme that plays when riding the Bicycle is a remix of the theme for Goldenrod City. This references the fact that you receive the Bicycle in Goldenrod City.
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Connection to Other Media
Earl, the teacher at the Pokemon Academy, will ask, "Want to be A Winner Is You?" This is a shout-out to the classic victory screen in Pro Wrestling.
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