If there was a class on the body tag which identified the Moodle, this would allow CSS files to be shared between Moodles, or Moodles and other web properties while still alllowing some specific styles to be applied to each Moodle.
The site shortname seems ideal for this, and should probably be appended with a string like "site-" or "moodle-" to prevent clashes. For example, on Moodle.org with shortname "moodle" it would look something like:
body class="moodle-moodle other-classes etc.
There may need to be a function that processes the shortname to make it CSS safe by removing odd characters etc.