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In pokemon Gold, Silver, and Crystal, if you turn on the Rocket Radio Signal at the Lake of Rage before catching Red Gyarados, you will be able to fish gyarados with the Good Rod 100% of the time.
In Pokemon Colosseum, if you snag the Shadow Johto Starter from one of the phenac city peons then let yourself get KO'd, the other two peons will have their Shadow Johto Starter missing from their party.
Makuhita and Hariyama are based on enemies from Mendel Palace. These are sprites of them, which are found in the Pokemon RS cartridge.
If you use Teleport to go from Rusturf Tunnel to Petalburg city, you can skip the rival battle in Rustboro city. If you do so, your rival will appear at Mr. Briney's cottage instead to fight you.
If you teach a Blastoise Mimic from Firered or Leafgreen, transfer it up to generation 6, mega evolve it, then have it Mimic a Kyogre's Origin Pulse, it will receive the benefits from Mega Launcher on Origin Pulse.
Relatedly, if you have a Diglett mimic Fly, it will become invisible when using Fly.
If a Pokemon that you transfer to a current game has a Ribbon from a previous game, it mentions it is a ribbon from another region. However, if it earned a ribbon from RSE and you transfer it to ORAS, it will instead say the ribbon was from a long time ago.
QR scan the windows 10 crash screen to get a Mareep pokedex entry.