Well, lets see... There are probably multiple Articuno/Zapdos/Moltres, since their "master" appearently can have babies. Mew is a peculiar case, but perhaps Arceus created it after Dialga, Palkia and Giratina, like the first form of life, you know, like the earliest forms of life, those small one-cell thingies, only more pink and cuddly. Right, so ancestor, hmm, I'd say there's only one Mew, or just a few, like 5 in the whole world. Obviously only one Mewtwo.
As the polar opposite of Lugia, it makes sense that there are multiple Ho-ohs as well. Same goes for the Beasts. Entei definately reproduce through roaring. Yes. Celebi is a tricky one, either there's only one who travels through time and helps itself, but that just seems confusing and stuff so I'm gonna go with multiple ones, but not that many, as mentioned before, something in the area of 20-30.
Multiple Golems, including Regigigas. There are probably multiple Eons too, "brother" and "sister" = genders = breeding. Now we get to some big ones. Quite obviously only one of each in the Weather Trio, as their powers are too great to be shared with others. I honstly don't have a clue on Jirachi, did it come from space? Though the whole "asleep for a millennium" thing could explain a few things if there are many. Deoxys comes from space and there are obviously many of them, but I'd like to take this further and say that another planet also has "pokemon" or similar creatures and that they sent out Deoxys as the perfect scout due to its forms, made clearly for survival. Oh, and just cuz it comes from space doesn't make it a legendary, but it's cool enough I guess.
Only one of each Lake Guardian, obviously only one of each part of the Creation Trio. Multiple Lunar Duos, I guessing multiple Manaphys (Guessing = I have no idea what so ever) and Phiones, as well as many Heatrans and Shaymins. And of course only one Arceus.
I think there are many Victinis and Meloettas, but only one Kami trio and only one of each Musketeer. The Tao trio is odd, their power are basically buffed up versions of the Birds, but with the lack of knowledge of Kyurem it's really hard to tell, so I'll let that rest. Genesect is not a legend! I will not accept it. How does taking a prehistoric giant bug and crossing it with a car make a pokemon legendary? That said, it shouldn't be able to "breed", and it's probably the only one, which is a good thing. *shivers*
Conclusion:
Multiple:Bird Trio and Lugia, Legendary Beasts and Ho-oh, Celebi, Regis, Lati@s, Deoxys, Cresselia and Darkrai, Heatran, Shaymin, Victini, Meloetta.
Only One:Mew, Mewtwo, Weather Trio, Lake Trio, Creation Trio and Arceus, Kami trio.
Unknown: Jirachi, Manaphy, Tao Trio.