The designs of five of the major Pokémon regions - Kanto, Johto, Hoenn, Sinnoh, and Unova - are strikingly similar in geography and demographics to regions in the real world. The first four regions are based on smaller regions in Japan, while Unova is based on the New York metropolitan area.
Main Regions
Kanto
The Kantō region of Japan is not only identical in name to Kanto in the Pokémon world, it is also very similar geographically; however, the western part of the game Kanto corresponds to eastern Chūbu.
Maebashi is the capital of the Gunma prefecture. In a neighboring of the city of Midori, there is the famous Iwajuku archeological site and the Iwajuku Museum.
The Tokyo Station is a train station located in Marunouchi in which the Tōkaidō Shinkansen, bullet train line that runs from Tokyo to Osaka, passes through.
In Japan, the Kanto region is often contrasted with Kansai, which is like Johto, to the west. However, Johto is geographically more similar to the combined region of Kansai and western Chubu.
Kinkaku was set on fire by a monk in 1950 (金閣寺放火事件). The wall is covered with gold leaf. Atop the Kinkaku temple sits a golden statue of a rooster or phoenix (Ho-Oh).
Hoenn is based on the southernmost parts of Japan - Kyūshū and Okinawa - with the latter highly condensed. (The distance between the northernmost and southernmost points of Okinawa is about as large as the distance between the northernmost and southernmost points of Honshu, the mainland of Japan.)
During the Edo period, among Europeans only the Dutch and the Portuguese were allowed into Japan, and then only at Nagasaki, specifically, Dejima. The main industry is shipbuilding.
Underneath the water's surface, ancient stone structures were found to be artificially created
Sinnoh
Sinnoh has been said to be an island like Hoenn, rather than a peninsula. It is based on the northernmost major island of Japan, Hokkaido. Part of Sakhalin (Japanese: 樺太 Karafuto) and Kunashir Island (Japanese: 国後島 Kunashiri Island), territories which are in dispute between Russia and Japan, are also included.
Unova has been said to be significantly distant from Kanto, Johto, Hoenn, and Sinnoh. Instead of being based on an area of Japan, Unova is based around the Manhattan area of New York City.
While the above locations are meant to correspond to the different regions of Japan, great liberties were taken with the design of their landscape. Some of the designers have admitted to drawing inspiration from real-world locations outside Japan, especially with locations shown in Pokémon movies.
While not mentioned specifically, Pastoria has some similarities with Boston and the surrounding area. A good portion of the city is built on fens, there are multiple national parks in the suburbs of outside the city, specifically in towns like Duxbury, Massachusetts and Marshfield, Massachusetts.
A village in the eleventh movie Giratina and the Sky Warrior, which was nearly destroyed by a glacier, is based on a town in Norway, which is threatened by the possibility of the mountain eroding into the fjord.
It's landscape, which is filled with huge pillar shaped rock formations resembles Meteora. Also, the architecture of the temples resembles that of ancient Greek temples.
It's modern buildings are based on the many new and modern buildings in parts of the city, and the Pokémon Baccer stadium is based on the ArenA, the city's local football stadium.
Mew was originally discovered in the jungles of the South American country Guyana. This is mentioned in logs inside of Cinnabar Island's Pokémon Mansion.
Xatu's FireRed, Silver, and SoulSilver Pokédex entries mention its association with mysticism in South America.
Poliwrath's Ruby, Sapphire, Emerald, Diamond, Pearl, and Platinum Pokédex entries mention its ability to swim the Pacific Ocean. Also, it is to be noted that the direction of its spirals depends on their geographical location.
Delibird's Ruby, Sapphire and Emerald Pokédex entries explain that a Delibird helped a famous explorer reach the top of Mt. Everest.
In Mewtwo Strikes Back, Team Rocket are disguised as vikings. In the English dub, Brock says that he didn't know that vikings still existed and Ash replies that they "mostly live in Minnesota." This is clearly a reference to the Minnesota Vikings football team.
Though in the Swedish dub of the movie, Ash replies to Brock that they come from Norway. Most likely referring to the Scandinavian Vikings that lived in the 8-11th century.
Ponyta's Pokédex entries mentions that it can clear Ayers Rock and jump over the Eiffel Tower in one leap. Tokyo Tower is referred in the original Japanese version.
In the English version of The March of the Exeggutor Squad, Melvin says he wanted to make it to Las Vegas. It should be noted that he said that he wanted to make it to Broadway in the Japanese version.
In the first movie, Meowth mentioned that they lived on the same Earth (although he may have been referring to the soil rather than the literal planet Earth).
In The Ninja Poké-Showdown, James says that the Fuchsia Gym looks like a Japanese restaurant.
In Pokémon Heroes, Misty makes a direct reference to the Earth stating that, "The Earth is so pretty."
In The Evolution Solution, Meowth says "Keep digging till you hit China!" to Jessie and James who were digging for clam shells.
Real world people and cultures mentioned
In Pokémon Shipwreck, Brock directly refers to the tale of Noah who sent a dove to find dry land after a great flood, according to some religions.
The main series games have featured staff members of Game Freak that typically reward the player for completing the National Pokédex, or occasionally through alternative methods. One in particular can actually be battled in-game.
Other applications of real-world locations
Mewtwo overlooking a "far away city" at the end of Mewtwo Returns
In all of the main series games, and some side series games, there is a Nintendo gaming console in the player's bedroom. This is a reference to the real world gaming company that owns the franchise.