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I own an adult male Crested Gecko, who I've had for about 3 years now, and he seems to be thriving. Recently though, I've noticed several teeny tiny black dots appear all over his body. I've read through several husbandry guides and they contain no information about this. I have no idea what they are and am wondering if its bad? Or even what they are exactly. If anyone has any information on this I would greatly appreciate your help.

Two things come to mind, one good, one bad. If he had never had any black dots on him since you owned him, I don't think crested geckos would suddenly develop a 'dalmation' pattern. So my second guess would be external parasites (ie mites).

As geckos are particularly sensitive to most mite treatments that I have heard off, may be difficult to ride them of mites, if that is indeed what the spots are. Isolate the one with these spots (if he/she is housed alone, move her as far away from your other geckos as possible). Take her out of her cage and put her in a small container with about an inch of water at the bottom to hopefully soak her (most likely she will just climb the side of the container but one can hope she will soak for a few minutes first) To make sure she has a place to get out of the water, other the sides of the container, place a rock or rolled up washcloth in the center.

WHile the gecko is soaking, take everything out of her cage, throw out any loose substrate (coconut husk, mulch, sand whatever), if using life plants, these may have to be tossed out too, or at least the dirt they are in with the roots and leaves well rinsed and repotted. Put the plant in direct sunlight for afew hours, watering as needed to keep the plant from wilting (if a shade plant, may not survive this process, the ideal is to kill mite eggs that may be in the leaf folds etc). Wooden branches, perches, hides etc, should be either soaked in a strong bleech solution and rinsed well then allowed to air dry for 24 hours (outside is best) or you can bake them in the oven at 250F for 2-3 hours, watch to make sure small peices don't catch fire.

For the cage and non-wood furniture, wash well in hot soapy water (dishsoap works well for this part). Then rinse. Fill with water again with all the furniture in the same container (if it all fits nicely) add one part bleech to 10 parts water (this is much stronger than normally used for disinfecting but this ensures any germs carried by the mites are killed). Soak for about 10 minutes, drain and rinse everything very well. Air dry for an hour or so, longer if necessary.

Keep in mind that some screens may not withstand the concentration of bleech, any not made of metal or fiberglass may disolve. If you have a cage you are not sure will withstand the concentration, use other anti-bacterial cleaner you may have on hand.

Once all the cleaning is done, put in papertowel and cage accessories (keep it minimal for now)

If your gecko did manage to soak in the water, if it indeed has mites, you should see a few floating dead in the water. If your gecko never touched the water or not that you know off, vasaline can be applied directly on the spots, but be careful not to get any on the underside of the feet or on the face. This will 'drown' the mites as well.

Prevent a mite is very useful against snake mites and other reptile mites, however, as I mentioned before, it can be very harmful to geckos. If your cage is wooden or mostly wooden, it may be necessary to use Prevent a MIte in the cage, but let it air dry completely in a well vented area (ie outside) before putting your gecko into the cage. I personally wouldn't risk it.

If you are not sure those dots can be mites, examine the dots under a magnifying glass. You should be able to tell they are oval insects or they are not part of the coloration of the scales, but embedded between the scales. If you are still not sure, take your gecko to a qualified reptile vet. They can get a closer look at what the spots are.
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PHLdyPayne