We used the following mod_rewrite rule:
RewriteEngine on
RewriteCond %{REQUEST_URI} !^/test/
RewriteCond %{REQUEST_URI} !^/my-folder/
RewriteRule (.*) http://www.newdomain.com/$1 [R=301,L]
This redirects (permanently with a 301 redirect) all traffic to the site to http://www.newdomain.com, except requests to resources in the /test and /my-folder directories. We transfer the user to the exact resource they requested by using the (.*) capture group and then including $1 in the new URL. Mind the spaces.