Lets see here:
It has been shown that all legendary birds (Barring Ho-Oh and Cresselia) can lay eggs (though I still wonder how one can't check their gender if they can check the gender of a Probopass), thought they're so rare and few that there's probably less then a hundred of each.
There are hundreds Celebi, though technically most of them are the same individual in different time periods. There have been at least two separate Celebi shown (at least in Mystery Dungeon there are two), though whether there are more is unknown.
Regigigas is most likely unique, but there are multiple copies of the other three Regis, one set Locked up in Hoenn, one Locked in Sinnoh, and possibly more in other locations, resting, awaiting to be discovered.
Mew is not a unique creature, but there are so few in the Pokémon world that it's difficult to spot multiple Mew. Mewtwo on the other hand, is considered unique as only one was created before the Cinnibar Mansion/Insert Anime Cannon Area Here was destroyed.
The weather trio (Rayquaza, Groundon, and Kyogre) are not unique creatures themselves, but the trio are considered to be the strongest members of their species. There probably are less then fifty of each left, though.
Manaphy is considered very rare, but there are colonies of Manaphy, and in turn there are even more Phione.
Shamin is perhaps the most "common" (by common I mean as rare as finding a Dratini, perhaps a bit more) legendary Pokémon other then Phione, it's just the fact that they're difficult to spot make them seem rare.
Deoxys is unknown, as so few have been spotted that it's difficult to find an accurate measurement of their population. There's at least three, though.
The three creatures of the lake (Azelf, Mesprit, and Uxie) are considered unique, even if it seems odd that the three beings that are responsible for making Spirit are located on a not-so remote planet.
There were once herds of Latias and Latios, but through some reason the population has been cut down drastically, with only a few remaining.
The dragon Trio (Dialga, Palkia, and Giratina) are considered unique Pokemon, but if the event following Arceus is considered canon (By the way, Arceus is unique), there might be one other individual among one of the three, possibly to take the place of the corresponding member of their kind in the case something happens to one of the main three. (Dialga's heart is said to keep time flowing, so there's got to be back-up in the case that Dialga is somehow slain.)
The legendary beasts are similar to the weather trio, in that there are a main set of individuals that make up the actual "trio" along with various lesser members of their species.
The way the PokéDex refers to Darkrai, there may or may not be more then one.
There are likely more Heatran in various other volcanoes around the Pokémon World.
...
And that's all I got...
