Using a custom domain with multiple Github repositories
It's possible to use a single custom domain with multiple Github repositories that use Github Pages. The available documentation makes it seem more complicated than it is, so this is an effort to provide some more simple instructions.
This post assumes you have a custom domain you want to use, and a Github account with one (or more) repositories that have a gh-pages branch. In my case tink.uk is the domain I want to use, and ljwatson.github.io is the root for the repositories that use gh-pages.
Create sub-domains for each repository
You need to create a custom sub-domain for each repository. To do this, you need to edit the zone file for your custom domain. The way to do this depends on where your domain is registered, so check out the help documentation provided by your domain registrar.
Add a CNAME record to your zone file for each sub-domain you want to create. I created four sub-domains for tink.uk, using the following CNAME records:
Example CNAME records
When you've added all the CNAME records, save your changes and make sure your custom domain is using the updated zone file.
Meanwhile, you need to configure each Github repository to recognise the sub-domain name you've just created for it. To do this, go to the Github page for each repository, and in Settings add the sub-domain to the Custom domain field (don't forget to save it).
Once the CNAME records have propagated, you'll be able to use the sub-domain to reference the gh-pages branch of your Github repositories. For example, design-patterns.tink.uk instead of ljwatson.github.io/design-patterns/.
Thanks to Dan Hopkins for his help.