From Bulbapedia, the community-driven Pokémon encyclopedia.
A Signature Pokémon is the most trusted Pokémon that a trainer has. Typically a trainer only has one Signature Pokémon (though there are instances of two or more), since they are considered to be the strongest on their team. Most Gym Leaders, Elite Four, and anime characters all have one, (such as Ash's Pikachu, or Lt. Surge's Raichu). Trainers tend to save their signature Pokémon for last, since it is the strongest on their team, and are often highly associated with the character.
In the Games
Kanto
Gym Leaders
Brock - Brock's Onix
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Reward: 1BP
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Misty - Misty's Starmie
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Reward: 1BP
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Lt. Surge - Lt. Surge's Raichu
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Reward: 1BP
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Erika - Vileplume
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Reward: 1BP
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Koga - Weezing
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Reward: $4300
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Janine - Venomoth
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Reward: 1BP
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Sabrina - Alakazam
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Reward: 1BP
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Blaine - Arcanine
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Reward: 1BP
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Giovanni - Rhyperior
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Reward: 1BP
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Elite Four
Lorelei - Jynx and/or Lapras
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Reward: $6600
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Reward: $6800
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Reward: $7000
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Reward: 1BP
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Reward: $11520
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Johto
Gym Leader
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Elite Four
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Reward: $7440
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Reward: $7740
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Reward: $7680
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Reward: $7680
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Team Rocket
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Reward: $1200
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Reward: $1320
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Reward: $2560
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Reward: $3040
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Notable Trainers
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Reward: $3840
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Reward: $3240
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Hoenn
Gym Leader
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Reward: 1BP
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Elite Four
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Reward: $4900
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Reward: $5100
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Reward: $5300
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Reward: $5500
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Reward: 1BP
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Reward: 1BP
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Team Magma
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Reward: $1920
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Reward: $1320
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Reward: $3120
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Team Aqua
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Reward: $1360
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Reward: $1720
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Reward: $3440
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Battle Frontier
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Reward: 18BP
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Reward: 16BP
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Reward: 16BP
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Reward: 20BP
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Reward: 15BP
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Reward: 13BP
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Noland has no signature pokemon.
Notable Trainers
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Reward: 3420
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Reward: $2740
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Reward: $2740
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Sinnoh
Gym Leaders
Roark - Rampardos
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Reward: 1BP
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Gardenia - Roserade
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Reward: 1BP
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Maylene - Lucario
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Reward: 1BP
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Crasher Wake - Floatzel
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Reward: 1BP
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Fantina - Mismagius
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Reward: 1BP
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Byron - Bastiodon
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Reward: 1BP
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Candice - Froslass
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Reward: 1BP
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Volkner - Electivire
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Reward: 1BP
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Elite Four
Aaron - Drapion
What's interesting to note about Aaron's signature pokemon is that it is not actually a bug type (like the rest of Aaron's pokemon), rather it is evolved from a bug type.
Bertha - Rhyperior
Flint - Magmortar
Lucian - Unknown, potentially Bronzong or Gallade
Cynthia - Garchomp
Team Galactic
Mars
Jupiter
Saturn
Cyrus
Battle Frontier
Notable Trainers
Barry
Dawn or Lucas
Unova
Gym Leaders
Cilan
Cress
Chili
Elite Four
Marshal
Team Plasma
Colress
Ex-Team Plasma
N - Zekrom (Black/Black 2) or Reshiram (White/White 2)
Notable Trainers
Hugh
Bianca
Kalos
Gym Leaders
Viola
Elite Four
Wikstrom
Team Flare
Aliana
Notable Trainers
Emma
Calem or Serena
International
Looker:
Red - Red's Pikachu
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Reward: 1BP
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