There are five control crystals in the Dark Depths, two of them can be obtained from the Underfjord the other three kinds are gained as a bonus from purchasing the pack (you get one free crystal) or from a level 1000 Dark Depths quest or as a bought extra from File > Buy Items > Amazing Items.
Lets deal with the two easy to obtain ones:
Pink Control Crystal
While the Fabricators construct the dungeon they often have excess supplies left over, rather than hauling these back to a central supply store they drop the supplies into a Recyclatron, these can be found throughout the dungeon and can be used to exchange loot items for raw resources or money.The Pink Control Crystal is needed to operate a Recyclatron.
Note: The Recyclatron will only accept Dark Depths items, that is expansion pack items such as Dark Depth chests, trophy rewards and prizes. So you can not take other items for example things you would normally deconstruct/dismantle and place them inside to get resources back … although you can still sell items here for money.
Green Control Crystal
The green control crystal will be used to access Shrines and other rest areas within the dungeon. These places will offer tranquility and buffage to any traveller who has the crystal.
Now the three rarer/harder to obtain crystals:
Red Control Crystal
Increase the chances of getting something good out of a Dark depths chest instead of the more common junk items, a 50% boost to chest diving.Gold Control Crystal
Increases money gained from monsters inside the Dark Depths by as much as 400%.Blue Control Crystal
When a monster spawns the likelyhood of it spawning with available loot items is increased by 15%. This includes powders (a required item for unlocking more areas of the dungeon).