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Topsites
Another form of rare Pokemon is Shiny Pokemon. During each wild Pokemon encounter, you have a 1/8000 of a chance of seeing in its alternative colors. They are VERY rare. How rare? You can play for 200 hours and only find three, not counting the given red Gyarados. The Shiny Gyarados is at the Lake of Rage.
Lapras is found deep within Union Cave (between Violet and Azelea) on Fridays. It is at level 20 and only one will appear every Friday.
After meeting Bill in Eruteak City's Poke-Center, head back to his house. If you have an extra slot in your party, he will give you a Level 20 Eevee. Otherwise, you will have to pay 6666 coins in Celadon City to get one.
Snorlax blocks Diglett's cave near Vermillion city. In order to wake it, you will need a Radio Card from both Johto and Kanto. Then, tune it into the Pokeflute channel and place it next to Snorlax. It is at Level 50.
Chikorita, Cyndaquil, or Totodile can be picked at the very beginning of the game. You'll receive just one from Professor Elm, so choose it wisely. You'll have to trade to get the other two.
Once you've completed your first gym, Elm's Aide will give you an egg at Violet's Poke-Center. If you have an extra slot open, he'll give it to you. Walk around and it will hatch into a Level 5 Togepi.
One of the houses in Cianwood contains a trainer who has just had a Pokemon stolen (most likely your rival stole it). If you have an extra slot available, he'll give it to you for safe keeping.
If you visit the Fighting Dojo in Saffron, you'll find out the Dojo's master is out training. Free an extra slot in your party, and travel deep within Mt. Mortar. You'll come across the Dojo's master. Defeat him, and he'll give you Tyrouge.
Once you awake them from their sleep in the Burned Tower, Raikou, Entei, and Suicune will travel Johto until you encounter them in tall grass. They are at Level 40 and will run unless you use Mean Look.
Lugia is located deep within the northeast Whirl Island. If you have the Silver Wing (complete Radio tower/Pewter City's old man) he will appear in a small room at Level 40 (Silver) or at level 70 (Gold). Silver's Lugia will know Aeroblast.
Ho-oh is located at the very top of Tin Tower. If you have the Rainbow Wing (complete Radio tower/Pewter City's old man) he will appear on the roof at Level 40 (Gold) or at Level 70 (Silver). Gold's Ho-oh will know Sacred Fire.