Talk to Munna in Easterly Town and you'll have the option to enter codes to unlock Pokemon that you have defeated. The codes and the corresponding toy Pokemon are indicated below. Keep in mind that they only work with the North American edition of the game.

2364-4610 - Articuno
0176-1458 - Audino
2159-4650 - Daring Eelectrik
3402-6465 - Dialga
5662-7748 - Fire Boost Enboar
3535-6928 - Gal
9625-7645 - Gli
0835-7338 - Grass Boost Snivy
7111-4427 - Grass Boost Serperior
0681-1611 - Groudon
0442-4822 - Lugia
8714-7361 - Moltres
7403-2240 - Oshawott
7746-3678 - Pikachu
4713-9936 - Speedy Unfezant
1959-4010 - Superstar Garchomp
6482-3610 - Tangling Stunfisk
2061-8332 - Tepig
8819-8699 - Thundurus
0250-7321 - Tornadus
6699-8898 - Victini
2452-2129 - Water Boost Samurott
1675-4459 - Zapdos
2153-6742 - Zoroark