Multisite: Other link color (css)
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