This article contains fan speculation.
There is no solid evidence for or against some parts of this article.

A signature Pokémon is a Pokémon which a Trainer is most commonly known for.

Criteria

Present on all teams: The Pokémon is on the Trainer's team in every possible encounter, or in the case of battle facilities, has the potential to appear on any given team.
Most appearances: The Pokémon appears on the most teams compared to any of the Trainer's other Pokémon. In the case of battle facilities with large pools of Pokémon for any given team, each species is only counted once, regardless of how many possible sets they can have.
Highest level when it appears: The Pokémon is at the highest level in the party every time that it appears.
Highest level most often: The Pokémon is at the highest level in the party more often than any of the Trainer's other Pokémon.
Owns multiple: The Trainer owns multiple Pokémon of the same species.
Holds item when applicable: The Pokémon carries a held item in every encounter in which the Trainer uses Pokémon with held items (ignoring battle facility teams, Mega Stones, and Z-Crystals).
Lead in the PWT: The Pokémon is always selected to be on the Trainer's team at the Pokémon World Tournament, and is sent out first.
Can Mega Evolve: The Trainer possesses the Mega Stone for the Pokémon in question.
Can use Z-Move: The Pokémon is carries a Z-Crystal in at least one encounter.
Appears on Sticker Template: The Pokémon appears alongside its Trainer on their respective Sticker Template.
Shadow: The Trainer has owned a Shadow Pokémon of this species.

Additional rules:

Each stage of an evolution line is counted separately for simplicity's sake.
Trainers with teams that depend on the first partner Pokémon chosen by the player have each encounter combined to prevent Pokémon gaining extra appearances.
Trainers with teams that depend on the version being played have each encounter combined to prevent Pokémon gaining extra appearances. Note that this only applies to paired versions, and not upper versions or remakes.
Black 2 & White 2 are assumed to be played in Challenge Mode.
Colosseum and XD: Gale of Darkness are assumed to be played optimally, catching every Shadow Pokémon as early as possible.
Rental Pokémon are ignored in all instances.

List of signature Pokémon

The following is a list of signature Pokémon, selected by which of them meets the most amount of criteria, ordered by their first battleable appearance. In the case of a tie, other material (such as Masters EX) will be referenced to break it, if possible. This list includes only notable trainers, such as Gym Leaders and Frontier Brains. Rivals have the Pokémon other than their first partner that meets the most the qualifications of a signature listed. Alternate universe versions of characters are combined with their main counterparts for the purposes of this list.

In the games

Generation I

Trainer	Pokémon	Notes
Brock	Onix	Present on all teams Highest level most often Holds item when applicable Lead in the PWT
Misty	Starmie	Present on all teams Highest level most often Holds item when applicable Lead in the PWT
Lt. Surge	Raichu	Present on all teams Highest level most often Lead in the PWT
Erika	Vileplume	Most appearances* Highest level when it appears* Highest level most often Lead in the PWT
Koga	Muk	Most appearances Holds item when applicable
Sabrina	Alakazam	Present on all teams Highest level when it appears* Highest level most often Holds item when applicable Lead in the PWT
Blaine	Arcanine	Highest level when it appears Highest level most often Lead in the PWT
Giovanni	Nidoqueen	Most appearances Highest level most often
Lorelei	Lapras	Present on all teams Highest level when it appears* Highest level most often Holds item when applicable
Bruno	Machamp	Present on all teams Highest level when it appears* Highest level most often
Agatha	Gengar	Present on all teams Highest level when it appears Highest level most often Owns multiple Holds item when applicable
Lance	Dragonite	Present on all teams Highest level when it appears Highest level most often Owns multiple Holds item when applicable
Blue	Exeggutor	Most appearances Can use Z-Move
Professor Oak	Gyarados	Highest level when it appears

Generation II

Trainer	Pokémon	Notes
Falkner	Pidgeot	Most appearances Highest level when it appears Lead in the PWT
Bugsy	Scizor	Most appearances Highest level when it appears Holds item when applicable Lead in the PWT
Whitney	Miltank	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Morty	Gengar	Present on all teams Highest level when it appears Highest level most often Owns multiple Lead in the PWT
Chuck	Poliwrath	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Jasmine	Steelix	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Pryce	Mamoswine	Most appearances Highest level when it appears Holds item when applicable Lead in the PWT
Clair	Kingdra	Present on all teams Highest level most often* Lead in the PWT
Will	Xatu	Present on all teams Highest level when it appears Highest level most often Owns multiple Holds item when applicable
Karen	Houndoom	Present on all teams Highest level most often
Janine	Venomoth	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Red	Venusaur	Present on all teams Can Mega Evolve Can use Z-Move
Silver	Sneasel	Most appearances
Li	Hoothoot	Present on all teams Highest level when it appears Highest level most often
Eusine	Electrode	Present on all teams Highest level when it appears Highest level most often
Proton	Golbat	Most appearances
Petrel	Koffing	Present on all teams Owns multiple
Ariana	Murkrow	Highest level when it appears* Highest level most often
Archer	Houndoom	Highest level when it appears Highest level most often

Generation III

Trainer	Pokémon	Notes
Roxanne	Nosepass	Most appearances Highest level when it appears Highest level most often Holds item when applicable
Brawly	Hariyama	Most appearances Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Wattson	Manectric	Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Flannery	Torkoal	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Norman	Slaking	Present on all teams Highest level when it appears Highest level most often Owns multiple Holds item when applicable Lead in the PWT
Winona	Altaria	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Tate	Solrock	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Liza	Lunatone	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Wallace	Milotic	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Sidney	Absol	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Can Mega Evolve
Phoebe	Dusclops	Highest level most often Owns multiple Holds item when applicable
Glacia	Glalie	Present on all teams Owns multiple Can Mega Evolve
Drake	Salamence	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Can Mega Evolve
Steven	Metagross	Most appearances Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT Can Mega Evolve
Brendan	Slugma	Most appearances
May	Wailmer	Most appearances*
Wally	Gallade	Most appearances Highest level when it appears Highest level most often Can Mega Evolve
Matt	Sharpedo	Most appearances Can Mega Evolve
Shelly	Mightyena	Most appearances
Archie	Sharpedo	Present on all teams Highest level most often Can Mega Evolve
Tabitha	Camerupt	Highest level when it appears Highest level most often
Courtney	Camerupt	Most appearances Can Mega Evolve
Maxie	Camerupt	Present on all teams Highest level most often Can Mega Evolve
Juan	Kingdra	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Anabel	Snorlax	Present on all teams
Tucker	Swampert	Present on all teams
Spenser	Slaking	Present on all teams
Greta	Umbreon	Present on all teams
Lucy	Seviper	Present on all teams

Generation IV

Trainer	Pokémon	Notes
Roark	Cranidos	Highest level when it appears Highest level most often Appears on Sticker Template
Gardenia	Roserade	Most appearances Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT Appears on Sticker Template
Maylene	Lucario	Most appearances Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT Appears on Sticker Template
Crasher Wake	Floatzel	Most appearances Highest level most often Lead in the PWT Appears on Sticker Template
Fantina	Mismagius	Most appearances Highest level most often Lead in the PWT Appears on Sticker Template
Byron	Bastiodon	Most appearances Highest level most often Lead in the PWT Appears on Sticker Template
Candice	Abomasnow	Most appearances Highest level most often Appears on Sticker Template
Volkner	Electivire	Most appearances* Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Aaron	Drapion	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Appears on Sticker Template
Bertha	Rhyperior	Most appearances Highest level when it appears Highest level most often Holds item when applicable
Flint	Magmortar	Most appearances* Highest level when it appears Highest level most often Holds item when applicable
Lucian	Gallade	Highest level when it appears Highest level most often Holds item when applicable
Cynthia	Garchomp	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT Can Mega Evolve Appears on Sticker Template
Lucas	Clefairy	Most appearances*
Dawn	Clefairy	Most appearances*
Barry	Heracross	Most appearances
Mars	Purugly	Most appearances Highest level when it appears Highest level most often Holds item when applicable
Jupiter	Skuntank	Most appearances Highest level when it appears Highest level most often Holds item when applicable
Saturn	Toxicroak	Most appearances Highest level when it appears Highest level most often
Cyrus	Weavile	Most appearances* Highest level most often Holds item when applicable
Cheryl	Blissey	Most appearances Highest level when it appears Holds item when applicable
Riley	Lucario	Most appearances Highest level when it appears Holds item when applicable Appears on Sticker Template
Marley	Arcanine	Most appearances Highest level when it appears Holds item when applicable Appears on Sticker Template
Buck	Claydol	Most appearances Highest level when it appears Holds item when applicable Appears on Sticker Template
Mira	Alakazam	Most appearances Highest level when it appears Holds item when applicable
Palmer	Dragonite	Most appearances*
Darach	Empoleon	Most appearances

Generation V

Trainer	Pokémon	Notes
Chili	Simisear	Most appearances Highest level when it appears Lead in the PWT
Cress	Simipour	Most appearances Highest level when it appears Lead in the PWT
Cilan	Simisage	Most appearances Highest level when it appears Lead in the PWT
Lenora	Watchog	Present on all teams Highest level when it appears Lead in the PWT
Burgh	Leavanny	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Elesa	Zebstrika	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Clay	Excadrill	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Skyla	Swanna	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Brycen	Cryogonal	Present on all teams Lead in the PWT
Drayden	Haxorus	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Iris	Haxorus	Present on all teams Highest level when it appears Highest level most often Holds item when applicable
Shauntal	Chandelure	Present on all teams Highest level when it appears Highest level most often Holds item when applicable
Marshal	Conkeldurr	Present on all teams Highest level when it appears Highest level most often Holds item when applicable
Grimsley	Bisharp	Present on all teams Highest level when it appears Highest level most often Holds item when applicable
Caitlin	Metagross	Highest level when it appears Highest level most often Holds item when applicable
Alder	Volcarona	Present on all teams Highest level when it appears Highest level most often Holds item when applicable Lead in the PWT
Cheren	Stoutland	Highest level when it appears Lead in the PWT
Bianca	Musharna	Most appearances
N	Zekrom	Most appearances*
Ghetsis	Hydreigon	Present on all teams Highest level most often Holds item when applicable
Ingo	Gliscor	Most appearances Highest level when it appears
Roxie	Scolipede	Most appearances Lead in the PWT
Marlon	Jellicent	Present on all teams Highest level when it appears Holds item when applicable Lead in the PWT
Hugh	Unfezant	Most appearances Holds item when applicable
Zinzolin	Cryogonal	Present on all teams Owns multiple
Colress	Klinklang	Most appearances* Highest level when it appears Highest level most often* Holds item when applicable Can use Z-Move

Generation VI

Trainer	Pokémon	Notes
Viola	Vivillon	Present on all teams Highest level when it appears
Grant	Tyrantrum	Appears most often*
Korrina	Lucario	Owns multiple* Can Mega Evolve
Ramos	Gogoat	Present on all teams Highest level when it appears
Clemont	Heliolisk	Present on all teams Highest level when it appears
Valerie	Sylveon	Present on all teams Highest level when it appears
Olympia	Meowstic	Present on all teams Highest level when it appears
Wulfric	Avalugg	Present on all teams Highest level when it appears
Malva	Pyroar	Present on all teams
Siebold	Barbaracle	Present on all teams Highest level when it appears
Wikstrom	Aegislash	Present on all teams Highest level when it appears
Drasna	Noivern	Present on all teams Highest level when it appears
Diantha	Gardevoir	Present on all teams Highest level when it appears Can Mega Evolve
Calem	Absol	Can Mega Evolve
Serena	Absol	Can Mega Evolve
Shauna	Goodra	Most appearances
Tierno	Corphish	Most appearances*
Trevor	Florges	Highest level when it appears
Aliana	Druddigon	Highest level when it appears
Bryony	Liepard	Present on all teams
Celosia	Manectric	Present on all teams
Mable	Houndoom	Present on all teams
Xerosic	Malamar	Highest level when it appears
Lysandre	Gyarados	Present on all teams Highest level most often Can Mega Evolve
Emma	Malamar	Highest level when it appears Highest level most often*
Aarune	Flygon	Present on all teams
Zinnia	Salamence	Present on all teams Highest level when it appears Highest level most often Can Mega Evolve

Generation VII

Trainer	Pokémon	Notes
Ilima	Smeargle	Present on all teams Highest level most often
Lana	Araquanid	Present on all teams Highest level when it appears* Can use Z-Move
Kiawe	Marowak	Present on all teams Highest level when it appears* Can use Z-Move
Mallow	Tsareena	Most appearances* Can use Z-Move
Sophocles	Togedemaru	Present on all teams Can use Z-Move
Acerola	Palossand	Present on all teams Highest level when it appears* Highest level most often Can use Z-Move
Mina	Ribombee	Most appearances* Can use Z-Move
Hala	Crabominable	Most appearances* Highest level when it appears* Can use Z-Move
Olivia	Lycanroc	Present on all teams Highest level when it appears* Highest level most often Can use Z-Move
Nanu	Persian	Present on all teams Highest level when it appears* Highest level most often Can use Z-Move
Hapu	Mudsdale	Present on all teams Highest level when it appears* Highest level most often Can use Z-Move
Molayne	Dugtrio	Present on all teams Highest level when it appears* Highest level most often Can use Z-Move
Kahili	Toucannon	Present on all teams Highest level when it appears* Highest level most often Can use Z-Move
Professor Kukui	Rockruff	Most appearances* Can use Z-Move
Hau	Raichu	Most appearances*
Gladion	Type: Null	Most appearances Highest level when it appears Highest level most often
Plumeria	Salazzle	Most appearances Highest level when it appears* Can use Z-Move
Guzma	Golisopod	Present on all teams Highest level when it appears*
Faba	Hypno	Present on all teams Highest level when it appears*
The Masked Royal	Rockruff	Most appearances
Sina	Glaceon	Present on all teams Highest level when it appears*
Dexio	Espeon	Present on all teams Highest level when it appears*
Ryuki	Turtonator	Present on all teams
Dulse	Poipole	Most appearances
Soliera	Poipole	Most appearances
Lillie	Comfey	Can use Z-Move
Trace	Pidgeot	Most appearances Can Mega Evolve
Green	Blastoise	Highest level when it appears Can Mega Evolve

Generation VIII

Trainer	Pokémon	Notes
Charm	Gengar	Present on all teams Highest level when it appears Highest level most often
Clover	Abomasnow	Present on all teams
Coin	Toxicroak	Present on all teams
Volo	Togepi	Most appearances

Generation IX

Trainer	Pokémon	Notes

In side games

Colosseum

Trainer	Pokémon	Notes
Justy	Nosepass	Present on all teams Highest level when it appears*
Wakin	Gloom	Owns multiple
Biden	Smeargle	Owns multiple Shadow
Gonzap	Skarmory	Most appearances Holds item when applicable Shadow
Folly	Whismur	Most appearances Highest level when it appears Highest level most often Owns multiple
Trudly	Makuhita	Highest level when it appears Shadow
Reath	Luvdisc	Present on all teams
Ferma	Yanma	Present on all teams Highest level when it appears*
Verde	Muk	Most appearances* Highest level when it appears Highest level most often
Rosso	Muk	Most appearances* Highest level when it appears Highest level most often
Bluno	Muk	Most appearances* Highest level when it appears Highest level most often
Skrub	Hitmontop	Most appearances* Holds item when applicable Shadow
Miror B.	Ludicolo	Most appearances Owns multiple
Dakim	Houndoom	Most appearances* Highest level when it appears*
Venus	Milotic	Most appearances*
Ein	Manectric	Most appearances*
Nascour	Metagross	Holds item when applicable Shadow
Evice	Tyranitar	Holds item when applicable Shadow
Willie	Linoone	Most appearances Highest level when it appears Owns multiple
Cail	Furret	Highest level when it appears Shadow
Vander	Whismur	Present on all teams Highest level when it appears*
Infin	Kyogre	Present on all teams
Inity	Salamence	Present on all teams