In the Dreamcast version of Sonic Adventure, there are some chao that are unobtainable in the newer versions. One of the most important is the original black chao, which was replaced in later versions with a monotone black chao. This chao can be used to mate with the gold and silver chao to get special chao. I haven't seen this elsewhere yet (and I don't have a clue why), so I'll post what I've found.
Gold chao + Black chao = Bronze chao (looks much like a gold chao, only much darker)
Silver chao + Black chao = Onyx chao (this one you may have heard of. It's a shiny chao that's very dark in color.)
Keep in mind that these special chao were not given their own colored eggs. The Bronze seems to hatch from gold eggs. I don't remember what color of egg the Onyx comes from.
As of yet, I have not found any other recipes that work. If you know of any others, please post them here. I've heard rumors that some other jewel chao are obtainable through breeding somehow. But if it's true, I do not know how to get them yet.
Here are some pictures of the Onyx and Bronze Chao.