I looked at alot of Bulbapedia articles, and came to this conclusion;
Poke-God, Palkia, Dialga, Ghost lizard thing, lake guardians: One of each.* Poke-God for obvious reasons...the Dragon's, since they all control a certain aspect of the universe, they also are unique. The lake Guardians should be obvious since there's only those three lakes that they dove into.
Golems: The anime and movies seem to indicate that there are more than one of each golem, but I'm not sure about the super golem thing.
Mewtwo: Given that it was cloned from mew and went berserk....it's a good guess to asume no one was stupid enough to make another one.
Mew: Probably multiple, but very very very rare.
Ocean whale, earth lizard and sky dragon things: Most likely only one given the nature they were hidden....it'd be pretty stupid to hide two in slumber while others still roamed around <.<
Manphy and Phione: Phione is obviously more since it can be bred, and manphy is in the same boat as Mew.
Celery: There is either one that can go back in time to create time clones of itself, or it is just as rare as mew.
Birds: Pokemon snap inticates that they are born from eggs so..... rare pokemon that are in alot of folklore
Beasts: Multiple, but are just as rare as the birds. The three Ho-oh revived in the GSC games are the only zombie ones, but otherwise the same.
Lugia and Ho-oh. Multiple just like the birds and beasts, but the two who stayed at the towers were very specific.
Dark Rye bread and Crossiont duck bird thing: There's at least two Darkrai...so there would logically be more.
Latios & Latias: Very rare, but still more than just the pair
Lava-monster: multiple since it has a gender
Rattata: Only one.
*Per dimension.