From Bulbapedia, the community-driven Pokémon encyclopedia.
Johto's regional Pokédex, a predecessor (note lack of numbers).
A regional Pokédex is a Pokédex order specific to a certain region of the Pokémon world. None of the regional Pokédexes yet released chronicle all Pokémon known (though the old Johto Pokédex did at its time, it is merely a precursor); instead they chronicle those Pokémon native to the region, starting with the Grass-type starter Pokémon, and followed by its evolutions, the Fire-type starter and its evolutions, and the Water-type starter and its evolutions, then continuing through the rest of the Pokémon native to the region. Legendary Pokémon of the region are typically placed near the end, while the very last spot or two are occupied by special Pokémon not normally encountered.
A regional Pokédex will often place newly released evolutions and pre-evolutions near their base form, no matter how much distance is between them in the National Pokédex. For example, in the National Pokédex, Aipom falls at #190, with its evolution Ambipom at #424. In the Sinnoh region's Pokédex, however, they are #063 and #064, respectively. Capturing all Pokémon in a regional Pokédex will cause the Game Freak developers in-game to award the player with a diploma in Generation I, Generation II, and Generation III. Completing the National Pokédex awards another diploma in Generation III. In Generation IV, seeing every Pokémon in the Sinnoh region's Pokédex allows the player to receive the upgrade to National mode from Professor Oak.
The Sinnoh Pokédex allows players to switch between regional and national views.
So far, however, only the Sinnoh region's original Pokédex does not naturally include all of the new Pokémon released in that generation. In Diamond and Pearl, Pokémon such as Gligar and Eevee were excluded from the listing, despite both receiving new evolutions in Generation IV and being easily available after getting the National Pokédex. The reasoning for this is unknown; however, both of these Pokémon, as well as all others that are relatives of a Generation IV Pokémon, among others, were added to the Sinnoh Pokédex in Platinum.
Generally regional Pokédexes are in the order of how the developers intend you to meet the included Pokémon within the main game, except for the Kanto and Johto Pokédexes which are put in seemingly random orders.
in the Unova regional Pokédex of Black and White
The Pokédex order for the six main regions of the Pokémon world are as follows:
The National Pokédex, which catalogs every Pokémon currently known, is as follows:
In the Pokémon Ranger series of spin-off games, Pokémon information is stored in the Browser, which acts similarly to a Pokédex for Pokémon Rangers. It is as follows:
In Pokémon Colosseum and Pokémon XD, the Strategy Memo acts as a Pokédex for Orre, listing Pokémon alphabetically.
Pokémon not native to a region which are obtained before a game's regional Pokédex has been upgraded to National Mode will be displayed with ??? as their Pokédex number in the status screen, where the regional Pokédex number is displayed in all other cases. If caught from the wild (through hacking the game), the Pokédex registration screen will display different numbers dependent on the game: Hoenn-based games display a number between 203 and 386, corresponding to the Pokémon's position in the National Pokédex minus those Generation I and Generation II Pokémon native to Hoenn (Arbok, for example, is #226, but Pikachu, Raichu, Sandshrew, and Sandslash, which appear in Hoenn, are skipped, making Nidoran♀ #227). Sinnoh-based games and Johto-based games, on the other hand, display the registered Pokémon as #000 if it is outside of their respective regional Pokédexes. Kanto-based games, interestingly enough, state only that the Pokémon's data has been registered, and skip straight to nicknaming the Pokémon, never displaying the Pokédex.