Mason from BGC (corporate boomer-man)
Galatea from BGC Tokyo 2040 (not really evil?)
Quincy from BGC Tokyo 2040 (creepy old man)
Kurei from Flame of Recca (not really really evil, candidate for creepiest bad guy awards, even creepy as a three-year-old
Bass from Violinist of Hameln (holds his head in the palm of his hand)
Sizer from Violinist of Hameln (not really a villian, carries a wicked scythe, golden wings stained with blood)
There's lots more but these are the ones I know of that have a villian-fan following.