Thankfully an email to the support guys at Github resolved the issue within a few hours. Still, I thought it might be a good idea to download my gists locally.
I can see all my gists as a JSON file online here:
Thus, I downloaded the file and thanks to the RJSONIO package I was able to clone all my gists locally with a few lines of R:
> sessionInfo() R Under development (unstable) (2012-10-19 r60974) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  RJSONIO_0.98-1