We added a special header to all outgoing repository and direct message notifications that should make it much easier to filter emails:
Direct messages get a List-ID of
user.github.com, while repositories get
repo.user.github.com. Do you want to easily filter all notifications from a user or organization? GMail supports wildcards too:
This is a quick workaround for those getting flooded with notifications. We feel your pain, and are discussing ways to solve this without drowning you in a sea of checkboxes.
Update: Gist comments now get a List-ID of