From your description it could be a few different things. Fungus growths (yellow fungus perhaps? though I haven't heard this form of fungus being green, though it bad cases it can appear a darkish yellow-brown). Burns can also appear dark and gangrene can look greenish.
I definitely suggest getting your dragon to a vet for examination and bloodwork. Bloodwork can tell if his white blood cell count is high, which indicates infection. A biopsy of the affected areas may be necessary for the vet to determine what is the case (ie: infection, virus, bacteria, fungus etc).
There is also some good information on a post not to far down with another dragon that had a dark spot on her head which may help you out as well. I have included a link to that thread below.
forums.kingsnake.com/view.php?id=1220437,1220437
To upload photos, you first need to use a hosting site, such as the kingsnake photo gallery. Once you have the picture on a website you can paste the link here in the message screen surrounded by the image tags (below the message window there is a link called tools and toys which will explain how you can use image tags).
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PHLdyPayne