I like the nested hidden boxes. I added to your page an example of formatting if the boxes were indented. If indenting is the route to go, then we should develop standard templates for each level:
{{dialog1|text}}
{{dialog2|text}}
etc...
This would give each level a standard color and indentation.
See, something like that is what I was thinking.
I could see an article going something like:
{{dialog|title=green text choice 1|text=contact response}}
{{subdialog|title=green choice 1|text=ipsum}}
{{undersubdialog|title=green undersub choice 1|text=hooray}}
{{undersubdialog|title=green undersub choice 2|text=bummer}}
{{subdialog|title=green choice 2|text=lorem}}
{{dialog|title=green text choice 2|text=alternate contact response}}
(cooler names might be needed).
Here the titles are your green text choices, the text is the contact response,
as well as a green text response IF there is only one. For example, above, in the second dialog (green text choice 2) there might be a green text response, formatted as normal with the *{{green|asdasdasdas}} (and even a following contact response).
If we do go the box route, I do agree that each box should be colored differently, but I think that each box's title should be colored green, as the titles would be the green dialog you select in the game window.
I could also see something like the mission objective template, which has space for primary, secondary, additional objectives, and the entrance and completion text.
The only problem with that is that I assume it limits the amount of categories, and unless there's a way to make a template ask you how many choices you want, and how many sub choices each main choice has, I think Zombie's idea of a template for each level of dialog choice is best.
Also, since we have no idea what content GR has, templates ought to be made for at least 4 levels of choice, in my opinion.
Somewhat unrelated: dialog vs. dialogue? Both are correct (I think), which should we use? Or does it even matter?