"Dark Caves" are just like normal caves/dungeons you encounter, they aren't necessarily any darker. The reason they are called "Dark Caves" is because there is an abundance of dark light floating out of the dungeon entrance. This is because there is a Dark Spore on that dungeon's final floor. Once the final-floor boss is defeated it will cough up the dark spore (which always takes three Pikmin to carry) so you can collect it as a treasure in the Research Pod. When the spore is engulfed by the pod it will lose the corrupting influence it had. There is one dark cave in each area, save for The Portal which only has one dungeon. Dark caves are generally the farthest from the landing site and take the longest to reach. They are the deepest in their respective area.