The Secret Champion is often a Former Champion, or Other Trainer, who can be found after Elite Four(or Kanto Gym Leaders in GSC), and is usually stronger than them.

Generation I

No one is the Secret Champion in Generation I.

Generation II

Pokémon Gold, Silver, and Crystal

In Generation II there is only one true Secret Champion, but I believe there is two.

Blue

Although technically a Kanto Gym Leader, since his status as a Former Champion, who can be found after the Elite Four, and is stronger than them. I Consider him to be a Secret Champion

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Red

The True Secret Champion

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Generation III

Pokémon Emerald

Steven is the Secret Champion of Emerald

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Generation IV

Diamond and Pearl

Palmer, being the Tower Tycoon, found after the Elite Four, and stuff, is the Secret Champion, however since he is a Frontier Brain in Platinum, He is no longer a Secret Champion

On 21st consecutive battle

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On 49th consecutive battle

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[[Pokémon HeartGold and SoulSilver and {{{2}}} Versions |HeartGold and SoulSilver and {{{2}}}]]

Red and Blue will be the Secret Champions. I don't have templates yet