All of my public presence runs as hundreds of separate GitHub projects. Because content, code, and JSON data drives my world, GitHub + GitHub Pages is a great way to run my operations. This approach to running my business, allows me to break up my research projects into small bit-size repositories, grouped into organizations, where I can collaborate with partners, and the public at large using GitHub's numerous social features — I call this Hacker Storytelling.
When I setup a new project, I first setup the master branch, making it public or private, depending on my goals. Then I always setup a gh-pages branch, to act as the public face for each project. Part of the process is always click next, and next through the default page, and templates part of the GitHub Pages setup flow. I always just choose the default settings, because once I've checked out the gh-pages branch, I immediately replace with my own template, depending on the type of project it is.
I have around five separate templates that I use, depending on if it is an API portal, and open data project, or a handful of other variations I use to collaborate around API related projects. I wish GitHub would let me specify my own templates, allowing me to add one or many template repositories, which could be used to spawn my new gh-pages projects. This would save me a couple of extra steps with the setup of each project.
I'm not sure how many projects, others GitHub users are setting up, or maybe I am just a special snowflake, but I can't help but think others would find this beneficial. As another more advanced feature, it would be nice to be able to have a reseller layer to this, where I could create account level template galleries, where my clients could then setup new organizations, and repositories, all driven my a master set of templates that I control.
Just brainstorming the possibilities here. It is what I do. If you happen to stumble across this post GitHub, it would be a sweet new feature, that I hope others would find valuable too!