Stone: stone is, along with gold, the two resources that you need to harvest all the time to create new buildings, traps and other stuff. It can be obtained from raiding other dungeons and stone collector sites.
Gold: Gold is mainly obtained from Gold Mines and also from raiding enemy dungeons, obtained as plunder after a successful battle.
Gems:the premium currency. You can get free gems by digging the ground, completing achievements, don’t expect to get a lot of gems though. Gems are used to speed up processes and upgrade some buildings.