DOMA and Prop 8. Both History.

[Alram]

Ignoring the content of Prop 8, and looking at only the procedures or events, we have, if I understand it correctly, a situation where the people in a state voted for and passed an amendment to their state constitution. The executive branch declined to enforce it or defend it in court. Those who were instrumental in getting the state amendment passed were found to have no legal standing.

This isn't really correct. I don't think there was any failure of enforcement, and the state defended it up to (but not including) the Ninth Circuit.

This would appear to set a precedent that the will of the people can be overturned by an indifferent executive branch or by non elected judges. Has this happened before? Is this a legal precedent that makes anyone else uncomfortable?

Here's where you go off the rails. A precedent? Like the Supreme Court hasn't ever, ever overruled anything, never gone against popular opinion? That's what they're there for, to ensure the rights of the minority are not trampled by the majority. The will of the people does not determine the rights of the governed.

Additionally, the unelected state of judges is intended to place them outside the pressures of pandering to political interests and place them above the fickle winds of public opinion. If you think electing judges is better, take a look at Texas.

As for the executive branch being indifferent, you say "indifferent", I say "principled", or more likely "politically savvy". They are, despite your rather obsolete sense of the "will of the people", bending to the will of the people by not defending Prop8.

The Executive branch in the state of California refused to defend the law in Federal court.

The SCOTUS ruling opens up the possibility for elected state officials to by refuse to enforce or defend ballot initiatives, leaving proponents of the ballot initiatives with no remedy. Justice Kennedy alluded to the same point in his dissent:

The Court’s reasoning does not take into account the fundamental principles or the practical dynamics of the initiative system in California, which uses this mechanism to control and to bypass public officials—the same officials who would not defend the initiative, an injury the Court now leaves unremedied. The Court’s decision also has implications for the 26 other States that use an initiative or popular referendum system and which, like California, may choose to have initiative proponents stand in for the State when public officials decline to defend an initiative in litigation...
the Court insists upon litigation conducted by state officials whose preference is to lose the case. The doctrine is meant to ensure that courts are responsible and constrained in their power, but the Court’s opinion today means that a single district court can make a decision with far-reaching effects that cannot be reviewed... here the Court refuses to allow a State’s authorized representatives to defend the outcome of a democratic election.”

This same mechanism or process could be used in another state to invalidate or strike down a referendum supporting gay marriage. So, instead of accusing me of using "obsolete" terms, should make a reasoned look at potential unforseen or unwanted effects that occur because of the way SCOTUS formulated its ruling.