The way i see it, the good and evil in Skyrim is more realistic then in regular RPG′s. Sometimes you have to look outside the box to find the meaning to some of the quests ect. In reality, good or bad is in gray shades rather then black and white. To truly know whats good or bad in this game so far is just like, in reality, based on how much effort you put in finding the truth and facts behind the dilemma. All the quests, NPCs and areas are filled with maps and lore that you can investigate to get a greater picture. In real life, we read in the papers that a man murdered a stranger in cold blood. The self righteous start to point fingers and such, but thru proper investigation it wasnt realy a murder, he was innocent, or it was an accident and so forth. The readers that do not take the time to look things up assume that he is guilty, and thus evil. Ive found that in Skyrim alot of things work the same way. Look things up, get a clear picture and then decide who is evil and not.
Take the Companions, as an example. At first glance, a religious fanatic, herald of good walk in, even tho the Companions are honorable they gasp when they find out they are werewolves and jump to the conclusion that they are evil. Personally, i think religious fanatic people are more evil then most, simply because they are brainwashed with religious views and what not and make assumptions based on information that they havent realy verified looked at properly, just assume its right cause "they" belive in it. Perhaps the information itself is from a preaching [censored] or a book made from people that arent even alive anymore. (Not long ago Rock was the devils music)

Even we assume that the werewolves are "evil" based on lore from stories outside the Skyrim universe. Look at the Silver Hand, the holy warriors with their silver blades, sworn enemies to the werewolves. They torture and skin people just because they have the "curse". If a good person, can turn into a beast, and remain in control. Isnt the beast itself good due to the nature of the person?
I could go on about this for a very long time, every quest and such so far has shown such depth as the one i discussed here.
Personally i find it refreshing to play a game with more depth then the usual blond male with a superhero chin kill [censored] that perhaps isnt evil at all, just because its black, hunchbacked and ugly with sharp teeth we assume its bad. Genocide in the name of holy light while cool music plays in the background. =)
In Skyrim, the "good guys" turn out not to be as good as we thought, just like when a catholic priest get caught IRL showing a unhealthy passion for young boys.