Ok i'll name all of them and what dungeon... Go to them with a 2 star party and they will usually ask. After you beat Rayquaza you will be able to recruit these.
Mt. Thunder Peak- Zapdos
Mt. Blaze Peak- Moltres
Frosty Grotto- Articuno
Magma Cavern Pit- Groudon
Sky Tower Summit- Rayquaza
Stormy Sea- Kyogre
Buried Relic- Mew (Give party leader music box defeat all pokemon and one is mew)
Pitfall Valley- Latios and Latias
Silver Trench- Lugia
Meteor Cave- Deoxys (Normal forme)
Fiery Field- Entei
Lightning Field- Raikou
Northwind Field-Suicune
Mt. Faraway- Ho-oh
Western Cave- Mewtwo
Wish Cave- Jarichi
Purity Forest- Celebi
Well thats all the legendarys but heres list of places to recruit rare but not legendary pokemon
Waterfall Pond
Grand Sea
Far Off-Sea
Joyous Tower
Unknown Relic
Ok thats all of them have fun recruiting!
Now known as Intoxication.