Legendary Trio

In each generation, there is typically at least one group of Legendary Pokémon that form a trio. Each Trio is seemingly subject to another Legendary Pokémon.

Generation I

 * Articuno, Zapdos and Moltres – The Legendary Birds, possibly led by Zapdos, ruled by Lugia.
 * Mew, Mewtwo, (Mewthree - manga only - and MechaMew2 - live only) - The Mew Trio/Quad, ruled by Mew itself.

Generation II

 * Suicune, Entei and Raikou – The Legendary Beasts, led by Suicune and ruled by Ho-oh.

Generation III

 * Regice, Regirock and Registeel – The Legendary Golems, ruled by Regigigas.
 * Groudon, Kyogre and Rayquaza – The Weather Trio. The leader and master of this trio is in fact, Rayquaza itself.

Generation IV

 * Uxie, Azelf and Mesprit – The Lake Trio, ruled by Arceus.
 * Dialga, Palkia and Giratina – The Creation Dragons, led by Giratina, and ruled by Arceus.

Generation V

 * Reshiram, Zekrom and Kyurem - The Tao Dragons, led and ruled by Kyurem itself.
 * Cobalion, Terrakion, and Virizion - Three Pokémon based on the titular characters of the novel The Three Musketeers. Out of these swords of justice, Cobalion is the oldest and wisest and is considered their leader.
 * Keldeo: The fourth member of the Swords of Justice, thus making them a quartet.
 * Tornadus, Thundurus, and Landorus - Based on three Japanese gods known as kami, with Tornadus based on Fujin, the god of wind, Thundurus on Raijin, the god of thunder, and Landorus on Inari, the fertility god. Landorus is the master of this trio.

Generation VI

 * Xerneas, Yveltal, and Zygarde - The Life Trio, led and ruled by Zygarde.

Pairs
Some of the remaining Legends fit into pairs, namely,
 * Mew Duo: Mew and Mewtwo
 * Tower Duo: Lugia and Ho-Oh
 * Eon Duo: Latias and Latios
 * Lunar Duo: Cresselia and Darkrai

Unnofical Trios
There are a few Legendarys that are fitted into trios by fans, but not officialy by Nintendo.
 * Mewtwo, Deoxys, and Darkrai - the Dark Trio. These three are similar in traits and seem to act as Generational counterparts to each other. They also have similar movies - with them beginning as villains but really being victims of circumstance.
 * Keldeo, Meloetta, and Genesect - the Event Trio. A group of three event Legendaries in Generation V.