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A perfect fail:
http://www.screencast.com/t/mHqVS5FMbdnq (see attached as well).
GitHub's buttons rarely work (e.g. format as code, italics, bold) -- I even submitted some bug reports to GitHub and they acknowledged that they had a problem, and then they proceeded to do absolutely nothing about it, so my confidence with them is pretty low.
The only markdown option that's remotely palatable is the AsciiDoc syntax:
http://www.screencast.com/t/jwKhUk8Ks1x
But again, the buttons there pretty much are useless, the "?" button includes instructions that are flat out wrong or devastatingly incomplete, and the manual formatting options are quite limited with AsciiDoc, so your documentation has to be constrained to simplistic outlines and your users suffer from loss of clarity.
GitHub acknowledged problems with its AsciiDoc parser specifically. I could go on, but really, I've wasted days of my life trying to make GitHub work and trying to get on board with it, but I've realized that it doesn't really have it where it counts in my opinion, and that's about as civil as I can be in my comments about it.