In crystal, you can catch Lugia (whirl islands), Ho-oh (tin tower), Suicune (is encountered throughout the game, but is ultimately battled in one of the towers in Ecruteak city), and last but not least, Raikou/Entei (roaming throughout the game.)
Lugia is in the whirl islands. Ho oh is in the tin tower. Suicune wanders around all over the place, but eventually stops.
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