As someone who enjoys the more traditional moral heroes (like Dresden) and more traditional stories where people are basically decent, and are distinct from the bad guys, I don't much like the more nihilistic fiction trend.
See I have to disagree with you on saying that Dresden is a traditional moral hero because he really isn't. There has been more than one occasion in the series where he has done some pretty morally questionable acts. When he took on the mantle of the Winter Knight he had to murder a helpless individual, or when he broke the snake guys legs with a baseball bat, these are not actions of the traditional hero.
Harry does have morals and he is a good guy but he is human which what makes him such a good character to read, he has moral quandaries and doubts and he feels bad about the ugly decisions he has to make but he makes them because he has too. The Knights of the Cross and Murphy are more traditional moral Hero's than Harry is.
As for the topic at hand I would have to say that I like to read both as long as they are written well. I love the LOTR where all the evil in the world was connected to Saron in some way and I like the Black Company books where the main characters spend most of their time fighting for the evil empire. having said that however, I would have to say that my favorite fantasy is like Dresden Files, where the main character isn't a saint while still maintaining the good guy persona.