It makes it easier to recognize that two or more comments in a long thread came from the same user.
This will be very useful if it makes it into GitHub Enterprise - our IT won't let us use Gravatar, so comment threads/issues are harder to follow.
Why won't they let you use Gravatar?
If you're running a recent version of GitHub Enterprise, the avatar base URL can be configured today. It's possible to run an internal, secure server that responds to Gravatar's URL scheme.
I filed a bug report that my default GitHub avatar was not found - Apparently it was an issue with broken profile images, and they fixed it with these identicons.