Mac OS X Applications Windows Stack Order When you right click an application in the dock, a list including the opened windows for that application is open, like this: http://cl.ly/image/350Q2J0q0e25

The problem is this: I would like to specify the ordering of these windows some way. Or at least understand what is the criteria for ordering these windows. I see no apparently logic for this window order.

Look the following: http://cl.ly/image/2I0E1A0y2A1q

The first window is in the desktop 3, in the second monitor. The second window in the desktop 4, in the second monitor. The third window is in the desktop 1, in the first monitor. There is no aparent logic, and they are not ordered by the most recent use, I'm sure.
Going by what I see on my Mac, and looking at your examples, it seems pretty certain that the order is alphabetical.  

I would expect that if there were a way to specify a different ordering, it would be under the Options submenu, but alas, there is nothing of the sort there.