Navel Rock and Birth Island are the so-called 8th and 9th island of the Sevii. They are both unlocked by going to event, which is now no longer available. Navel Rock has Ho-oh and Lugia, while Birth Island has Deoxys (Attack Forme).
Some Pokemon from 2nd gen can be found in Altering Cave if E-Reader data is put into the game.
Unown can be found on 7 Island after you push all the rocks in a small cave into their position.
Mewtwo can be found in Cerulean Cave like original Pokemon Red (after you beat E4 the 2nd time).
That's all I can recall.