You obtain them by mutating berries, which basically involves planting specific types of berries next to each other, and then it has a chance of giving you a certain EV berry (and some others too).

Untill now we know the following combinations:

Mago + Iapapa = Pomeg

Chesto + Persim = Kelpsy

Sitrus +Lum = Tamato

Aspear + Leppa = Hondew

Aguav + Figy = Grepa

Oran + Pecha = Qualot

(and some other non EV berries, not listed)

Source: http://www.serebii.net/xy/berryfields.shtml