Well, I guess you mean "Soul Silver", and the main legendary Pokemon is Lugia, Water/Flying-Type.
Moltas: the fire legendary bird Pokemon the second strongest bird Pokemon
the only legendary that you can breed is manaphy. and that will result in a phione.
You can't breed legendary Pokemon eggs on Pokemon SoulSilver or on any Pokemon game.
Latios
They will simply gain Exp. You can't breed legendary pokemon.
It might depend on the Pokemon, though usually you can face legendary Pokemon again if you beat the Champion.
over 9000
no
Raikou, Entini,ho oh, lugia, kyogre
it is impossible except for when you have cheats in Pokemon pearl,platinum,diamond
If you saved your game before catching the legendary Pokemon reset the game that way you can try catching it again.
to find lugia go to the 4 whirl islands