Route 38 and 39 in gold and silver, and route 43 on crystal
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You can only catch Zapdos in Crystal by cheating. otherwise it is not in the game
Find the crystal onix, make it weak and catch it with your best ball
Rayquaza isn't in Crystal.
you don't catch articuno in crystal but you can get one from red, blue or yellow.
You can't catch Mewtwo in Gold, Silver, or Crystal. But you can catch it in HeartGold and SoulSilver in the Cerulean Cave at Lv70.