Anotsu Kagehisa (Blade of the Immortal)
He's just plain likeable, just wants to be strong, but lets his subordinates offend everybody in the process.
Sesshoumaru (Inu-Yasha) Did I spell his name right?
He isn't necessarily a bad guy, but definitely an obstacle. Always keeps his cool, and I like how he sneers and bullies his younger brother. Totally justifiable. =P
Light Yagami (Death Note)
I almost forgot how much I liked this guy until I looked through this thread. I rooted for him because he had really pure intentions to do good, but in the "wrong" way..... Kind of like Batman.