List of all items in Heart Gold and Soul Silver and locations.
List of all items in Black and White and locations.
List of items in Black and White 2 and locations.
List of all items in X and Y and locations.
To find a specific item in a Generation click on the link and hold Ctrl + F, then type in the item your searching for.
Master Ball
Heart Gold and Soul Silver:
Location: New Bark Town
Requirements: Talk to Professor Elm after earning all eight Johto Badges.
Heart Gold and Soul Silver:
Location: Goldenrod Radio Tower
Requirement: Match all 5 numbers in the Pokémon Lottery Corner.
Black and White:
Location: Opelucid City
Requirement: Meet Professor Juniper in town after earning all eight Unova Badges.
Black and White:
Location: Castelia City Pokémon Center
Requirement: Talk to a man after the player has outsider Pokémon with at least 50 different original Trainers.
Note: The man will no longer give out gifts after the Master Ball.
Black 2 and White 2:
Location: Mistralton City
Requirements: Meet Professor Juniper for the first time in town.
Black 2 and White 2:
Location: Plasma Frigate
Requirments: Defeat Colress after entering the Hall of Fame.
Black 2 and White 2:
Location: Join Avenue
Requirment: Grand prize from Raffle Shops.
Note: The higher the shop's rank, the higher the chance of getting a rare prize.
X and Y:
Location: Poké Ball Factory
Requirement: Defeat Celosia and Bryony.
Note: The player is given a choice between the Master Ball or a Big Nugget, but receives both items regardless of their choice.
X and Y:
Location: Loto-ID Center
Requirement: Win the highest prize.
Note: The player have to match all the five numbers in one ticket.
Source: http://bulbapedia.bulbagarden.net/wiki/Master_Ball
Rare Candy
Heart Gold and Soul Silver:
Johto: Route 34, Violet City, Ecruteak City (With Dowsing MCHN), Olivine City (With Dowsing MCHN), Radio Tower (Earn 25 Points at Buena's Password), Mt. Mortar (With Dowsing MCHN), Mt. Mortar, Tin Tower, Whirl Islands (With Dowsing MCHN), Whirl Islands (With Dowsing MCHN), Mt. Silver (With Dowsing MCHN), Shining Lighthouse
Kanto: Route 27, Route 28 (With Dowsing MCHN), Vermillion City (Fan Club President), Cinnabar Island (With Dowsing MCHN), Indigo Plateau (With Dowsing MCHN), Cerulean Cave (With Dowsing MCHN), Victory Road, Pickup, Pokéathlon Dome (Monday and Saturday)
Shops:
Johto: Battle Frontier, Pokeathlon Dome
Pokéwalker: Sinnoh Field (5000+ Steps), Sightseeing (5000+ Steps)
Black and White:
Route 2, Route 3 (With Dowsing Machine), Route 13, Route 16, Pinwheel Forest (With Dowsing Machine), Desert Resort (With Dowsing Machine), Nimbasa City, Mistralton Cave, Chargestone Cave, Twist Mountain (With Dowsing Machine), Icirrus City (Winter Only), Anville Town, Victory Road, Abundant Shrine, Lostlorn Forest, N's Castle, Pickup, Pokémon Café Forest, Rugged Mountain
Shops:
Gear Station
Battle Subway
Black and White 2:
Route 3, Route 3 (With Dowsing Machine), Route 8 (With Dowsing Machine), Route 12 (With Dowsing Machine), Route 18 (With Dowsing Machine), Dreamyard, Pinwheel Forest (With Dowsing Machine), Castelia City, Castelia City (Sunday - Defeat Seven Trainers on Royal Unova), Moor of Icirrus, Village Bridge, Abundant Shrine, Route 20 (Autumn Only), Route 22, Route 23 (With Dowsing Machine), Virbank City, Relic Passage, Strange House, Seaside Cave, Victory Road B2W2 (With Dowsing Machine), Victory Road B2W2, Nature Preserve, Pickup, Black Tower/White Treehollow (Area 6-10 reward)
Shops:
Join Avenue (Raffle Shop reward)
Battle Subway
PWT
X and Y:
Route 13, Route 16, Route 16, Route 17, Parfum Palace, Ambrette Town, Couriway Town, Victory Road, Lydsandre Labs, Route 18, Pickup, Route 18 (from Psychic Inver), PokeMiles
Shops:
Battle Maison
Source: http://serebii.net/itemdex/rarecandy.shtml
http://bulbapedia.bulbagarden.net/wiki/Vitamin
I may have went a little excessive on this answer.
Hope I helped :)
