>>16517712Rule of thumb, Box legendaries (and relatives) are totally unique pseudo-dieties that are one of a kind, while most Trios (except the Lake Trio) are super rare, but multiples.
There are exceptions. Lugia, if Orre is considered, has multiples out there (Anime too due to the babby Lugia). Then there's the HG/SS event for Groudon/Kyogre/Rayquaza, though that could just be the Orbs attracting them ALL the way from Hoenn to there.
Dialga is another iffy one, there's no complete confirmation the Dialga from Platinum is (timeline fuckery not withstanding) the same Dialga from the Mystery Dungeon games. But it's highly likely Dialga, Palkia, Giratina, Arceus, and the Lake Trio, are all uniques.
By story we know for a fact that Kyruem, Reshiram, and Zekrom are uniques. Other legendaries are unconfirmed and possibly multiple. Really only god-like 'mons seem totally unique (plotwise anyway, stats notwithstanding)