I think a good villain should be complex. As bad as some of the stuff Doc Ock has done (and keep in mind that his character has been VERY inconsistent through the years), I don't think he'd just watch a building collapse while everyone inside died. Nor would Kingpin just turn the other way if he saw a car about to hit a child. (Keep in mind that the Kingpin in the mini is much younger version and in less power than the one in the comics today). Are these two characters now 'good guys' because they showed a shred of decency? No, but they're a lot more interesting.

For instance, in the ending of the current Ultimate Spider-Man arc Fisk came across as a lot more noble than Black Cat. Whereas Kingpin was using fairly legit means (although he did have Dini rough up the museum owner) to aquire something for a noble cause (his wife) Black Cat was all about petty revenge on something Fisk probably had nothing to do with.

I think a villain who ends up doing mostly bad things yet has a shred of decency, a villain who you love to hate you sometimes sympathize for, is much more interesting to read than some nutjob who's bad just for the sake of being bad.