Thieves' Town/Swamp Palace/Lorule Castle
There's a small, destroyed house in the southwest corner of Thieves' Town. Lorule's first baby is attached to a wall there.
The next baby is actually in the grass surrounding the Bomb Flower at the Bomb Flower Shop just south of town.
Head to the Rupee Rush game. A baby is attached to the northern cliff wall there.
Now head to the Octoball Derby game. Break up the trio of skulls near the baseball diamond to reveal a baby inside one. Morbid, eh?
This is one is high up on a cliff wall directly south of Octoball Derby. You'll need to use the equivalent rift in Hyrule to reach it.
Head for the Swamp Palace, but stop by the swampy water just north of the dungeon itself. In the deep water here is another baby.
Southeast of the Swamp Palace is a trio of columns with a baby atop. Use a Pegasus Boots charge to knock it loose.
Head directly north to find another baby attached to a cliff wall.
Continue north. Between the Vacant House and the Octoball Derby is this boulder. Lift it to discover a baby beneath.
To the east is the Vacant House itself. Check the ledge behind the house to discover an attached baby.
Head north to Lorule Castle. The first tree to your right has a hidden baby inside. Use a Pegasus Boots charge to reveal it.
This is attached the right wall of the Lorule Castle gate.
Head west to the Blacksmith. This is attached to the left side of the house.
By the Fortune Teller to the north are several boulders. Lift them to discover another baby.
From the Blacksmith, head west to reenter Thieves' Town. Use a Pegasus Boots charge on the first tree you see to pop a baby out from inside its branches.