PokéBase - Pokémon Q&A
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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.

Also there is a Raquaza Event in Japan for B/W.
In mystery dungeon ble and red he's found at sky peak and the other ones also sky peek but you need wonder codes for time and darkness and the rank that you get from scizor in sky