A refugium that is often mentioned here is a separate "tank" or area of the sump that can store animals that would get eaten in the main tank. This area can have many versions and layouts. Some people have pretty display refugiums for people to see other animals and for some it is all about filtration and hidden in the sump. Deep sand beds, 'pods, cheato, and reverse lighting aren't often pretty to look at.
Many people put marco algae in there refugium. It acts like a natural filter. I have heard of people turning off there protine skimmer because there refugium did such a good job at cleaning the water. It also reduces the growth of bad algae and increases coraline alge growth. A refugium also adds to the total amount of water you have in your system.