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Thanks for the kind words Eric.
I don't think there will be an issue removing your domain folders
from /sites. The key table to check is the 'system' table, which
stores references to module and theme paths. If there are no
references to your unused domains there, you should be ok.
One way to check this safely is to edit your hosts file locally,
specifying your localhost IP for your production domains. You can then
request your site with its public URL, but it will be served from your
local machine. With that done, test the effect of removing each of the
directories in turn.
If you do run into some trouble, I would first run /update.php
(from the web, not drush), and then try registry_rebuild: https://drupal.org/
Let us know how you get on.
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