Genesect's backstory is similar to Mewtwo's. Both were created by villainous teams in at least one canon (Team Rocket for Metwto and Team Plasma Genesect), and genetically engineered and enhanced to be more powerful.

Prime numbers had a significant role in the composition of N's battle theme. Though there is little evidence to suggest this in-game, N is actually a mathematical genius. It can also be said that he sees the world in a 'black and white' fashion, using formulas to make sense of it.
Composer and director Junichi Masuda frequently references this in N's battle theme with the use of prime numbers, and even more so with the addition of sounds like a clock ticking in N's final battle theme.

The GTS has a filter to prevent Pokémon with inappropriate nicknames from being traded. However this prevented Pokémon, such as Cofagrigus, from being traded without nicknaming it because their name contains a keyword. This has been mostly fixed but some Pokémon, such as Nosepass, are still unable to be traded without a nickname.

On Route 10 in the original Pokemon Red and Blue, Picnicker Carol gives a description of a chunky, pink Pokemon with a floral pattern. This description is what Munna was based on.

The Sword of Justice legendaries are inspired by the Three Musketeers.
Cobalion, Terrakion, and Virizion are based on Athos, Porthos, and Aramis respectively, while Keldeo is similar to the youngest Musketeer, d'Artagnan.

There is an unused stone in the game's code called the God Stone. A gray recolor of the Light Stone/Dark Stone sprite, with the description "A phantom stone."

In the Café Warehouse in Nacrene city, by looking at middle or right tile of the door, pressing A will show a message saying: "It looks like a cabinet full of Pokémon goods."

TM67 Retaliate & TM94 Rock Smash both have a sprite oversight where the TM Sprite does not match the Type in the HUD.
Retaliate is a Normal move but is shown as a Dark Type in the Sprite.
Rock Smash is a Fighting move but is shown as a Rock Type in the Sprite.

Game Freak spent a year and a half developing the story and characters for Pokemon Black & White.

According to the Pokedex entry for Darumaka in Pokemon White, people used to keep themselves warm by putting its droppings in their clothes.