When using the same theme on multisites, what would be the easiest sollution to give each domain another link color?
I would suggest you try Domain CSS module if you are already using Domain Access module. ( https://drupal.org/project/domain_css )
This will give you ability to add additional css per domain so you can keep everything clean and organized.
Another alternative is to write a custom module and get $_SERVER['HTTP_HOST']; which you can run into switch statment to load css.
Similar question: Load domain-specific CSS file on a multisite