Ho-Oh - Bell Tower
Lugia - Whirl Islands
Raikou, Entei - roaming Johto
Suicune - roams Johto and Kanto
Articuno - Seafoam Islands
Zapdos - Power Plant
Moltres - Mt. Silver
Mewtwo - Cerulean Cave
Kyogre or Groudon (depending on game) - Embedded Tower with Orb (from Mr. Pokemon)
Rayquaza - Embedded Tower with Jade Orb (from Prof. Oak when you show him Groudon and Kyogre)
Latios or Latias (depending on game) - roaming Kanto after National Dex
You can get Dialga, Palkia and Giratina if you have the special event Arceus.
There may also be other pokemon available in events and over wi-fi. They had a Mew given away over wi-fi in Japan recently so that will probably come to other countries soon.