The Github Wiki allows you to use different format parsings, so I fast-checked the differences between 3 of them.
The options: AsciiDoc, Creole, Markdown, Org-mode, Pod, RDoc, Textile, reStructuredText
The ones I checked: Creole, Markdown, Textile.
And that’s already my preferred order: Creole over Markdown over Textile.
Creole is an attempt to standardize wiki markup, as before Creole wikis were just using something and not the same. The result, 1.0, is pretty good.
The first thing you’ll notice for example is that, in contrary to the others, you’ll mark italics, and not just emphasis.