Void Crystal (Light-blue). You will gain them every day If you are a guild member. The number of Void crystals given depends on a guild level. You can also buy 5 void crystals for every guild member for 2000 gems. Entering a Raid costs 1 Void crystal.
Life Crystal (Green). They are bought for the gems only. For the 1000 gems every guild member gain 1 Life Crystal (or 5 Life Crystals for 4000 gems). Life crystals are used to enter Rainbow's Lair. Entering a Lair once cost you 2 crystals.
Fire Crystals (Red). They are granted as a reward for a certain place in a Guild Wars. For example, every member of a first place guild gain 100 Fire Crystals. Fire crystals are awarded once per week after Sunday. You can use them to open Guilds Crypt X5. Opening a crypt costs 5 Fire crystals and allow you to draw 5 creatures.
You can see the amount of Void, Life, and Fire crystald in the Raids tab in the Guild Screen.
Dark Crystals (Dark-blue). The only crystal that is not guild-oriented. You gain Dark Crystals for reaching certain place in PvP Rankings. 2 first players in monthly rankings gain 80 crystals (40 crystals in weekly), other gain lower numbers. They are awarded before 1 day of a month for monthly personal ranking and before every Thursday for weekly personal ranking. Dark Crystals are used to open Rankings Crypt X5. Opening a crypt costs 5 Dark crystals and allow you to draw 5 creatures.