We added a special header to all outgoing repository and direct message notifications that should make it much easier to filter emails:

Screenshot of an email with a List-ID header in GMail.

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:

Screenshot of GMail's filter interface.

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 ID.gist.github.com.