How to get Kyogre- After you get seven badges fly to Sootoplois City and you will find Steven and he will escort you to the Cave of Origin. (P.S.) Save before you fight him and carry a LOT of Ultra Balls.
How to get Groudon- Same thing as Kyogre.
How to catch Latios and Latias- These are your legebdary birds Latias (Sapphire) Latios (Ruby)you find them after you beat the game. You also can catch them on southern island.
How to get Milotic- Catch Feebas and give it max beauty stats.
How to get Rayquaza- He is in Sky Piliar.
How to get Pikachu- You catch him in the first patch of grass in the Safari Zone.
How to get Phanphy- This is really hard, you find him in the secret area in the Safari Zone you need to have Acro Bike and jump across th white rails.
How to get Heracross- Find him in the same area as Phanphy.
How to get Nosepass- Find him Granite Cave by smashing rocks.
How to get Snorunt- You find this Pokemon in Shoal Cave he is very hard to find.
How to get Flygon- First catch a Trapinch in the dessert then evolve twice and it will become a Flygon.
How to get Salamance- First catch a Baggon in Meteor Falls the go surfing up the Water Fall go through some ladders then there should be a hidden back room and when you enter there eill be some land then surf again go strait the you will find more land get on it keep walking around and eventually you will run into a Baggon, baggon evolves around LV.30 into Shellgon then at LV.50 it will evolve into Salamance!
Get Castform- Save the Weather Institute from Team Aqua/Team Magma and the prof. will give you him, you CAN NOT catch him he his almost like Lapras, an experiment.
The easy way to get Jirachi- buy the bonus disk for Pokemon Colleseum and download him.