Below is a list showing where which puppy can be found.

Numbers
World
Where to find them?
01, 02, 03
 Traverse Town Behind the Mystical House
04, 05, 06
 Traverse Town Red Trinity next to Item Shop
07, 08, 09
 Traverse Town Desk in Item Workshop
10, 11, 12
 Traverse Town In front of stairs at the Secret Waterway
13, 14, 15
 Wonderland Hedges in the Queen's Courtyard
16, 17, 18
 Wonderland The trees of the Lotus Forest
19, 20, 21
 Wonderland On the Hedges of the Tea Party Garden
22, 23, 24
 Olympus Coliseum Blue Trinity Mark at the entrance
25, 26, 27
 Deep Jungle On the Trees in the Hippo's Lagoon
28, 29, 30
 Deep Jungle Vines Area 2
31, 32, 33
 Deep Jungle Blue Trinity in the Climbing Trees
34, 35, 36
 Deep Jungle Blue Trinity at the Camp Site
37, 38, 39
 Agrabah Inside Aladdin's House
40, 41, 42
 Halloween Town On the Bridge
43, 44, 45
 Neverland Clock Tower Near Wendy
46, 47, 48
 Agrabah Palace Gates
49, 50, 51
 Agrabah Cave: Entrance
52, 53, 54
 Agrabah Treasure Room
55, 56, 57
 Monstro Chamber 3
58, 59, 60
 Wonderland Pot in the Bizarre Room
61, 62, 63
 Hollow Bastion Grand Hall - Second time there
64, 65, 66
 Halloween Town Moonlight Hill
67, 68, 69
 Halloween Town Guillotine Square
70, 71, 72
 Halloween Town Guillotine Square
73, 74, 75
 Monstro Mouth - on a Platform near Gepetto
76, 77, 78
 Monstro Chamber 3
79, 80, 81
 Monstro Champter 5
82, 83, 84
 Neverland Central Ship
85, 86, 87
 Neverland Ship: Hold 4
88, 89, 90
 Neverland Captain's Room
91, 92, 93
 Hollow Bastion Raising Falls
94, 95, 96
 Hallow Bastion Lift Stop
97, 98, 99
 Hollow Bastion High Tower
Rewards

Rewards depend on how many puppies you bring back to Pongo and Pedrita, below is a list of how many puppies you need for each reward.

Puppies Needed
Items
12
 Curaga-G
21
 Firaga-G
30
 Thundaga-G
42
 Mythril Shard
51
 Torn Page + Mythril
60
 Megalixir
72
 Orichalcum
81
 Ultima G
90
 Ribbon
99
 Power of Wind + All Gummi Blocks