Good to see GitHub finally leave Helvetica and go for a custom font family. There’s not yet an official announcement of the change from their blog, though I’m not sure we should expect it.
There’s nothing inherently wrong with a site going with a standard font like Helvetica or Georgia, but with services like Google Fonts and Typekit, there are many great new fonts from which to choose.
It’s also interesting how the font family on GitHub is determined by your environment. Here’s one person whose instance looks dangerously close to Comic Sans. It’ll be interesting to see how GitHub reacts to all of the community feedback, and whether they keep this dynamism. If they do, it will be also interesting to see whether other sites adapt a similar approach. GitHub has a lot of influence because its customer base is programmers and designers — the sorts of people who get to decide how the rest of the web should look.