I'm posting this here, because I found it rather handy. We're gonna have to team up to take some of these out.
http://www.bluegartr.com/threads/117575-Beta-4-Minion-ListFor all your pokemon needs
Baby Bun
Rewarded for completing the FATE "Lazy For You" with a Gold Medal rating in the East Shroud, by Castrum Oriens (X?, Y?)
Baby Raptor
Purchased from Auriana for 125 Allagan Tomestones of Philosophy in Revenant's Toll, Mor Dhona (X22, Y8)
Purchased from Boughberry Trader for 2400 gil in Redbelly Hive, South Shroud (X22,Y17) after the successful completion of the FATE chain "Clearing The Hive"
Cherry Bomb
Purchased from Bango Zango for 2400 gil in Limsa Lominsa Lower Docks (X9, Y11)
Purchased from Maisenta for 2400 gil in Old Gridania (X?, Y?)
Purchased from Roarich for 2400 gil in Ul'dah - Steps of Nald (X10, Y9)
Coblyn Larva
Gathered by Miner. Level46-50 Log Entry. Northern Thanalan, Blue Fog. Details
Dust Bunny
Purchased from Auriana for 125 Allagan Tomestones of Philosophy in Revenant's Toll, Mor Dhona (X22, Y8)
Fledging Dodo
Purchased from Auriana for 125 Allagan Tomestones of Philosophy in Revenant's Toll, Mor Dhona (X22, Y8)
Gravel Golem
Crafted by Goldsmith. Level46-50 Recipe. Difficulty: 93. Durability: 80. Wind Shard x99, Astral Rock x3.
Kidragora
Gathered by Botanist. Level 46-50 Log Entry. East Shroud, ???. Details
Mammet #001
Purchased from Bango Zango for 2400 gil in Limsa Lominsa Lower Docks (X9, Y11)
Purchased from Maisenta for 2400 gil in Old Gridania (X?, Y?)
Purchased from Roarich for 2400 gil in Ul'dah - Steps of Nald (X10, Y9)
Model Vanguard
Crafted by Goldsmith. Level46-50 Recipe. Difficulty: 93. Durability: 80. Wind Shard x99, Garlean Steel Plate x1, Garlean Steel Joint x1
Smallshell
Rewarded for completing the FATE "It's not Lupus" with a Gold Medal rating in Eastern La Noscea, south of Costa del Sol (X?,Y?)
Tiny Rat
Purchased from a vendor for 2400 gil in Highbridge, Eastern Thanalan (east of Drybone) after the successful completion of the FATE chain "Attack On Highbridge"
Wayward Hatchling
Purchased from Bango Zango for 2400 gil in Limsa Lominsa Lower Docks (X9, Y11)
Purchased from Maisenta for 2400 gil in Old Gridania (X?, Y?)
Purchased from Roarich for 2400 gil in Ul'dah - Steps of Nald (X10, Y9)
Wind-up Airship
Rewarded for completing the level15 Main Scenario Quest: The Gridanian/Ul'dahn/Lominsan Envoy.
Wind-up Aldgoat
Crafted by Weaver. Level 46-50 Recipe. Difficulty: 93. Durability: 80. Lightning Shard x99, Vanya Silk x1, Twinthread x1, Chocobo Feather x1.
Wind-up Dullahan
Crafted by Armorer. Level46-50 Recipe. Difficulty: 93. Durability: 80. Water Shard x99, Darksteel Nugget x3
Wind-up Qiqirn
Crafted by Weaver. Level 46-50 Recipe. Difficulty: 93. Durability: 80. Lightning Shard x99, Vanya Silk x1, Twinthread x1, Chocobo Feather x1
Notes
-You can purchase the old Hamlet items (coke, potash, etc) for 100 Allagan Tomestones of Philosophy each in Revenant's Toll (Mor Dhona)
-You can get Allagan Tomestones of Philosophy by trading gear with cracked materia on it to the Calamity Salvager. Doublemelds and triplemelds give the most tomestones.
-Planning on adding in-game pictures eventually, feel free to post yours
Unknown/Unconfirmed Sources
Gigantpole
Morbol Bulb
Tiny Tortoise