After you obtain the Masterball enter a battle with a trainer that has a shadow pokemon. With your first Pokemon, use the Masterball. With your second Pokemon, select BAG and hit Y or X and switch its position with a different type of Pokeball. You will successfully snag the Pokemon and retian your Masterball.
You can transfer Jurachi from the Pokemon Colosseum Bonus Disc into a GBA. Then just transfer him into Pokemon Colosseum.
Raikou can be found as a Shadow Pokemon of Cipher Admin Ean in the Shadow Pokemon Lab.
Suicune can be found as a Shadow Pokemon of Cipher Admin Venus in The Under.
Entei can be found as a Shadow Pokemon of Cipher Admin Dokim.at the top of Mt. Battle.
Purify all 48 Shadow Pokemon and beat 100 trainers in Battle mode on Mt. Battle using only your Story Mode Pokemon team.
Beat Deep King Agnol in the Deep Colosseum with all the Shadow Pokemon. You will get a message about someone attacking people with a Shadow Togetic, so go to the Outskirt Stand and fight him.
Thanks to Revolution readers Pokefreak, cappie, and Robert Hernandez!