Main Series Games - Ruby/Sapphire/Emerald (Sky Pillar) - HeartGold/SoulSilver (Embedded Tower) - Omega Ruby/Alpha Sapphire (Sky Pillar) - Ultra Sun/Ultra Moon (Cliff World; Ultra Space Wilds) - Sword/Shield's The Crown Tundra (Max Lairs) - Brilliant Diamond/Shining Pearl (Ramanas Park) - Scarlet/Violet's The Indigo Disk (Great Crater of Paldea with the Rayquaza Treat)
Main Series Games (Outdated Events) - Diamond/Pearl - Black/White - X/Y - Omega Ruby/Alpha Sapphire - Scarlet/Violet
Most people that ask these questions don't care about the side series games. If this doesn't apply to you, you may find this information here.
In the games Ruby, Sapphire, Emerald, HeartGold, SoulSilver and in Pokemon Mystery Dungeon. Hope This Helps! :)
--------------->See you in the above games ^
I don't think you can Catch Rayquaza in Pokemon Mystery Dungeon, though.