I know this wasn't directed primarily at me but the greyness of Robb, Ned and possibly Jon (although certainly not as much as the others) is related to their short-sighted focus on honour and loyalty, regardless of how damaging it will be. Ned is by far the easiest way to demonstrate this whereby his focus on being honourable has had devastating impacts on his entire family. He could have swore loyalty to Joffrey immediately as Cersei requested or sided with Renly and, while discussing the impacts of these choices we'd be getting into unfounded hypotheticals, he would not have endangered his entire family as much as stubbornly refusing out of honour and knowingly being branded a traitor; a rather selfish and inconsiderate act which would taint the family name. He did, ultimately, break his honour for the better of others but it was (clearly) too late. The same can be argued for the murder of Daenerys which he went against because it was an dishonourable decision but in order to prevent a future invasion it was the right choice. With Robb, there are similar events such as the beheading of the Carstark elder because it was the 'just' thing to do, ignoring the huge ramifications that it could lead to. He endangered everything out of a belief in justice and did so because it was merely his belief, despite the large opposition to the decision. The Starks (primarily Ned, Robb and, to a lesser extent, Jon Snow) believe they're doing the right, just, and honourable thing in many cases and as isolated instances maybe they are right, but as a collection of events it's almost narcissistic as they endanger countless others for self satisfaction.
With regards to Joffrey, he's probably one of the few 'non-grey' characters on the show but if you wish to find sympathy within him it would be as a result of his formation, why he is as he is; warring parents, growing up incredibly spoilt and without control, being filled with dreams of grandeur, a domineering grandfather and spiteful mother both obsessed with preserving the family lineage with a drunken father (or should that be step-father) who continuously boasted about his heroism and the lives he had taken/violence he had committed. As for Cersei and Tywin, their primary 'good' characteristics are related for the wish to preserve the family lineage and legacy with a deep desire to improve the 'situation' for themselves and their children. This does, unsurprisingly, end up as a flaw as they are as recklessly focused on this as the Starks are on honour and they pay the price by being incredibly unhappy but there is an always an awareness of the impact of the choices they make, they don't view decisions in a bubble.
There's actually quite a contrast in the Starks and the Lannisters in this way I feel. The Starks, seemed, extremely content in themselves (well, Catelyn, Robb and Ned while simultaneously ignoring their grief) but were in a rather poor situation, seen as treacherous, their home destroyed and having suffered large casualties (almost wiped out with this episode). The Lannisters on the other hand are mostly unhappy (Cersei unhappy with her approaching marriage, Tyrion unhappy with his, Tywin unhappy with his nephew, Joffrey the only happy one of them all) but have themselves placed in an excellent situation for the family; ruling the land, dominating almost the entirety of Westeros (Stannis and the Greyjoys are the only people in open rebellion if I haven't misremembered) while they are incredibly rich and have suffered few casualties (actually, I can't remember any Lannister dying with the exception of the two children by Carstark).
I don't think it's really fair to look at one house as 'good' and one as 'bad'. Both of them have significant flaws. Both of them have good intentions, the Starks' honour and nobility and the Lannisters' desire to improve their family's status, but they both bring about a plethora of flaws.
EDIT: Although, I don't think every character is 'neutral', there's an entire spectrum of characters. If all of the characters were neutral/good/bad, the show would be bland. The diversity is part of what makes it (I feel) particularly good, and many characters (and there are 'many characters') so compelling (I'm ignoring that this can be perceived as a negative for the show in the belief that it struggles to balance the characters well which I'd somewhat agree with but seems to fall under 'pacing' as opposed to a problem with the characters themselves).
:/ I want Arya to kill Joffrey
