Legendary Pokémon

Many Pokémon are legendary or very rare. You can't usually catch them with a Pokéball. You have to use a Master Ball, Netball, etc.

Legendary Dogs
Entei
Suicune
Raikou

Legendary Birds
Zapdos
Moltres
Articuno 

Legendary Spirits
Uxie
Azelf
Mespirit

Legendary Earth
Kyogre
Groudon 

Legendary Regi's
Regigigas
Registeel
Regice
Regirock

Sky Legendary
Rayquaza

Eons
Latias
Latios

Tao Trio
Reshiram
Zekrom
Kyurem

Deoxys Forms
Deoxys Normal
Deoxys Speed
Deoxys Defense
Deoxys Attack
Others (Ones with no category.)
Heatran
Palkia
Dialga
Girtina
Cresselia
Shaymin Land Form
Shaymin Sky Form
Jirachi
Victini
Mew
Mewtwo
Xerneas
Yveltal
Terrakion 
Keldeo

PLEASE TELL ME IF I MISSED ANY!