(from April, 2009)
The ability to break forks or reverse the direction of forks.
(from July, 2009)
The ability to add contributors to a repo before you've pushed anything (you can do it if you know the admin URL but there's no link).
EDIT: this has now been resolved.
(from September, 2009)
GitHub should calculate Leidel numbers and show them on user profile pages.
(this was mostly a joke)
(from August, 2010)
(via brosner) GitHub should make use of git push -u in pushing instructions for a new repo.
EDIT: this has now been resolved.
(from May, 2011)
Support for folders for my repos rather than a flat list under my username.
(reiterated July, 2012)
Ability to organize my repos into folders
(from January, 2012)
The ability to annotate branches.
(from February, 2012)
The ability to fork a repo more than once (to different orgs or personal+org)
EDIT: this has now been resolved.
(from February, 2012)
(via lukeman) A replacement for the traditional project mailing list.
(from June, 2012)
Let you trivially attach gaug.es to your user, org and repo pages (I mean on their site, not github pages)
EDIT: I guess this has been resolved, at least for repos with Traffic Analytics although that doesn't seem to cover the user / org level.
(from June, 2012)
Web hooks per user / org
(from July, 2012)
Distinction between "bookmarking" an interesting project and "subscribing" to updates in my feed about it
EDIT: this has now been resolved with watching vs stars
(from July, 2012)
Auto dismiss notifications that have already been actioned (e.g. if PR already merged, don't show it any more)
(from February, 2013)
If you change which fork is the official one on GitHub, migrate over stargazers and watchers.
(from March, 2013)
Ability to assign tickets to non-collaborators. Otherwise, the "fork to contribute" model does not work well with issues.
(from May, 2013)
contributor agreement signing
(from July, 2013)
A DON'T MERGE flag on pull requests for works-in-progress.
EDIT: I wonder if this is now possible with labels.
(from July, 2013)
Take an issue and automatically convert it into a branch and WIP pull-request.
(from August, 2013)
(via Gary Dusbabek) a "sync this fork to upstream" button.
(from October, 2013)
(via Adam Baldwin) private issues and pull requests for open source projects to improve responsible disclosure of security issues
column numbers (or even better, a ruler) in the text editor to help keeps lines within a limit.