I could only think of one "main" merit badge to add to Stuart's collection: a variant of the Rules Tinker badge.
I use Bare Bones rules. I don't just tinker with the rules, I strip 'em, using only a limited number of classes, simplified combat, and fewer modifiers and subsystems.
The Bare Bones badge will also go well with some of the exception badges I'm going to do later. For example, if you have a Classes badge with the Bare Bones badge, it means your game uses fewer classes, races, or ability scores.
This badge was made using a couple images from Lorc's RPG icons set. Just like Lorc's icons, it's licensed under a Creative Commons Attribution 3.0 Unported License.