Build what's next on GitHub, the place for anyone from anywhere to build anything.
Join us October 28-29 in San Francisco or online for GitHub Universe, our flagship developer event uniting people, agents, and the world's code.
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…
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 ID.gist.github.com.