As far as I could tell, Black edition is just simply a different paint job on the mobo (not everyone is a fan of the Yellow/Black color scheme of UD5H/UD3H, and not many hardware actually have a matching color scheme either).
Comparing the specs, the main highlights between the different models are:
UD3H is narrower than UD5H, hence UD3 only has 6 mounting screw holes where as UD5 has all 9 for a standard ATX board.
Number of system fan headers, number of back IO USB3.0 ports, Physical BIOS switch, PCI layout, LAN sockets, supported RAM Speed, Marvell SATA Ports and onboard debugging code display are the main things that stand out to me as different between UD3H and UD5H.
I went with UD5H because I like having mounting the motherboard with 9 screws rather than 6.