I will list all the made up locations, with the cities/islands/towns/etc. in bold.
Note: Not including nameless places, places only spoken of or places where the region is unknown.
Places are listed by region, then in alphabetical order.
Kanto
-Bill's Lighthouse
-Cameran Palace
-Camomile Island
-Camp Pokéhearst
-Chrysanthemum Island
-Commerce City
-Cremini Town
-Dark City
-Evolution Mountain
-Fennel Valley
-Gaiva Dam
-Gardenia Town
-Grampa Canyon
-Gringey City
-Hidden Village
-Hollywood
-HopHopHop Town
-House of Imite
-Leaf Forest
-Maiden's Peak
-Metallica Island
-Mossgreen Village
-Mt. Hideaway
-Mulberry City
-Neon Town
-New Island
-Old Shore Wharf
-Pokélantis
-Pokémon Land (island)
-Pokémon Ninja School
-Pokémon Tech
-Pokémon Theme Park
-Pokémopolis
-Porta Vista
-Potpourri Island
-Rifure Village
-Rota
-Sable City
-Sayda Island
-Scissor Street
-Silver Town
-Stone Town
-Sunnytown
-Team Rocket Academy
-Team Rocket HQ
-Terracotta Town
-Tree of Beginning
-Wisteria Town
-Xanadu Nursery
Orange Archipelago
-Ascorbia Island
-Butwal Island
-Cleopatra Island
-Fairchild Island
-Fire Island
-Golden Island
-Grapefruit Island 1
-Grapefruit Island 2
-Grapefruit Island 3
-Grapefruit Island 4
-Grapefruit Island 5
-Grapefruit Island 6
-Grapefruit Island 7
-Hamlin Island
-Ice Island
-Kinnow Island
-Kumquat Island
-Lightning Island
-Mandarin Island
-Mikan Island
-Moro Island
-Murcott Island
-Navel Island
-Pinkan Island
-Pummelo Island
-Rind Island
-Shamouti Island
-Sunburst Island
-Tangelo Island
-Tarroco Island
-Trovita Island
-Trovitopolis
-Valencia Island
Johto
-Alto Mare
-Arborville
-Battle Park
-Big Town
-Bloomingvale
-Bluefinland
-Blue Lagoon
-Blue Moon Falls
-Blue Point Isle
-Bonitaville
-Castalia City
-Charicific Valley
-Diglett Village
-Dragon Holy Land
-Eggseter
-Florando
-Greenfield
-Happy Town
-Inland City
-Lake Lucid
-Lake of Life
-Lake Slowpoke
-Len Town
-Marine Pokémon Laboratory
-Marion Town
-Maroon Town
-Megi City
-Mount Quena
-Ogi City
-Ogi Isle
-Onix Tunnel
-Palm Hills
-Palmpona
-Pokémon Jugitsu Academy
-Pudgy Pidgey Isle
-Red Rock Isle
-Remoraid Lake
-Remoraid Mountain
-Scarlet City
-Secret Garden
-Silver Rock Isle
-Silver Town
-Slowpoke Temple
-Snowtop Mountain
-Sunflora Lodge
-Transit Town
-Way Away Island
-Whirl Cup Colosseum
-Whitestone
-Wobbuffet Village
-Yellow Rock Isle
Hoenn
-A-B-C Islands
-Banana Slakoth Garden
-Bomba Island
-Camurupt Point
-Crossgate Town
-Donto Island
-Foothill Town
-Forbidden Forest
-Forina
-Izabe Island
-Kiri-Kiri Mountains
-Lake May
-LaRousse City
-Maisie Island
-Mirage Kingdom
-Monsu Island
-Muscle Island
-Oldale Ruins
-Purika City
-Rinshin Town
-Riyado Town
-Rubello Town
-Shroomish Forest
-South City
-The Greenhouse
-Togepi Paradise
-Valley Of Steel
-Volley Town
-Wailmer Island
-Wales Island
-Wazoo Island
Sinnoh
-Alamos Town
-Amber Castle
-Arrowroot Town
-Beach Rose Town
-Bewilder Forest
-Brussel Town
-Camellia Town
-Celestic Town Historical Research Centre
-Chocovine Town
-Crown City
-Dandelion Island
-Daybreak Town
-Diablo's Ocean
-Dustox Flower Field
-Emeragrove Field
-Eterna Historical Museum
-Gracidia
-Greenstation Town
-Lake Psyduck
-Lily of The Valley Island
-Lilypad Town
-Majolica Town
-Metagross Mountain
-Michina Town
-Mt. Shady
-Neighbourly Town
-Pokémon Summer Acadamy
-Sandalstraw Town
-Shelter Town
-Space-time Tower
-Squallville
-Summit Ruins
-Sunyshore Tower
-Xatu's Forest
Unova
-Absentia Natural Park
-Ambiga Town
-Antimony Research Lab
-Area 28
-Astilbe Town
-Clock Tower
-Eindoak Town
-Ferroseed Research Institute
-Hero's Ruin
-Kingdom of the Vale
-Litwick Mansion
-Luxuria Town
- Milos Island
-Mistralton Tower
-New Tork City
-Nimbasa Town
-Pokémon Hills
-Rainbow Valley
-Roshan City
-Stonesthrow Town
-Sword of the Vale
-Vertress City
-Village of Dragons
-White Ruins
-Windy Station
Decoloure Islands
-Capacia Island
-Cave Island
-Frond Island
-Grand Spectrala Island
-Harvest Island
-Honey Island
-Paladin Island
-Scalchop Island
-Torom Island
-Wayfarer Island
Kalos
-Allearth Forest
-Agivnon Town
-Brackish Town
-Calenthe Town
-Diamond Domain
-Grace Tower
-Kalos Canyon
-Lagoon Town
-Odyssey Village
-Orsay City
-Pokémon Summer Camp
-Pomace Mountain
-S.S. Cussler
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