I assume the mascots of gen's 3-5 (possibly gen 6's too) are one of a kind, oh and Arceus (Arceus has been shown to create the creation trio so they likely don't breed.)
It's beleived the Kyogre from Fiore is the one from Hoenn after Emerald so I like to assume it (and Groudon, and Rayquaza) move around.
Lugia and the birds likely aren't as it appears they have nests. Entei neither as it's dex entry implies one is born when a volcano errupts.
And Heatran proably isn't either nor [email protected]