The Wind Cries Mary

I believe the lyrics of this song are multilayered and can also be interpreted in a multitude of ways, but I will try to break them down how they seem to work imho:

"After all the jacks are in their boxes and the clowns have all gone to bed"

The jacks (pieces of the children's game, jacks) are put away because the players grew tired of playing. The game of jacks is the game people play in life to be the "best" or the "winner" (such as war), regardless of who loses in their wake. The players are the clowns, though, because they, themselves, eventually lose and just go to bed (or even die).

"You can hear happiness staggering on down the street footprints dressed in red"

So when the game ends, the people whose voices are heard are those left in the wake who were not playing the game. And they continue happily on the path of righteousness, although staggering. Their blood can be seen in their footprints while they still walk the path. They are visibly harmed, but do not divert.

"And the wind whispers Mary"

"Mary" is Mary of Bethany from the Bible. (Mary walked the path of peace and faith, in contrast to her sister Martha, who lived in selfishness and doubt.) Hence, the wind now quietly speaks her name, the wind being the age or the times.

"A broom is drearily sweeping up the broken pieces of yesterday's life"

Those who are left after the fighting try to pick up the pieces of their destroyed way of life.

"Somewhere a queen is weeping Somewhere a king has no wife"

The queen is sad because the man she married is not the great man she believed he was. He was only a malevolent leader orchestrating senseless fighting for his own gain. She leaves him after the fighting because he has nothing left to offer her.

"And the wind, it cries Mary"

The people who played and lost the game, like the king and queen, have lost almost everything. So the wind is louder now, crying for change.

"The traffic lights, they turn up blue tomorrow and shine their emptiness down on my bed"

The traffic lights are the old leaders, like the king and queen, who used to tell you when to go and when to stop. People followed their directions because it got them to where they were headed. But now, the traffic lights are turned blue (sad because they lost their power). Those who followed the traffic lights are now also blue because they have no direction for the future. Even the narrator is awoken by the empty blue.

"The tiny island sags downstream 'cause the life that lived is, is dead"

The great kingdom that was is now only a "tiny island." It is isolated and all the pieces that are left fall apart without its surrounding structure. The old society that once thrived is now totally dead.

"And the wind screams Mary"

The wind is so loud now, that it cannot be ignored.

"Will the wind ever remember the names it has blown in the past?"

The narrator questions whether the wind will consider the names it has blown before, such as kings' names, or perhaps Martha's name.

"And with this crutch, its old age, and its wisdom it whispers no, this will be the last"

The wise, old, wind now has Mary as its crutch to keep on flowing while the people get together to repair and build a better place to live in. The wind whispers to the narrator (so the people don't hear and become complacent) that this is the last name that needs to be blown. The people finally recognize the error of their ways.

"And the wind cries Mary"

The wind calms a bit but still cries Mary for the stragglers. Perhaps later the wind will quiet down and no longer need to blow Mary's name, when the people realize their happiness and harmony depend on their own actions.