Redcloak, once lackey and now evil genius in his own right in Rich Burlew's excellent Order of the Stick, is possibly my favorite evil mastermind of all time. I like that he is pragmatic, reasonable, not prone to grand gestures, and has a solid dose of love and protectiveness for his own people. It's that last part that really sells me on Redcloak, and even though he's nominally a bad guy, puts me on his side much of the time.
You can read a surprisingly extensive Wikipedia entry on Redcloak here. And if you're not reading Order of the Stick, you should be.