One clear way to distinguish between a good organization and a bad one is to look at how it handles disagreement.
The mark of a good organization is that disagreement leads to improvements in the business.
The mark of a poor organization is that disagreement leads to a worsening in the business.
In the chaos and uncertainty of the startup environment, disagreement is inevitable. Good organizations make sure that disagreements are heard, and that the relevant team members work together to find an acceptable resolution.
In contrast, bad organizations either fail to focus, or end up battling internal rather than external foes.
The temptation exists to ignore disagreements and simply hope that they go away. This may seem attractive, but becomes quickly untenable. Startups don't have the resources or the time to vacillate or pursue multiple approaches. Everyone has to agree and work towards a single focus.
I've seen teams of smart, talented people who didn't have the discipline to resolve their disagreements, and they almost always head south.
Remember, of course, that resolution doesn't have to mean that everyone agrees...what it does mean is that everyone agrees on what course of action the company will pursue--even those who disagree. You can't let people employ the passive-aggressive approach and just take their ball and go home.
As a side note, I feel that a lack of disagreement is also a warning sign. Given that there are seldom clear right answers, a startup that lacks disagreement is either not trying, not thinking, or not composed of human beings. A talented team consists of people with different backgrounds and skills--they are bound to disagree on some things. The trick is how you handle those disagreements.