Existe um software de terceiros para o Windows (IIS), que - além de outras coisas - faz esse trabalho muito bem: ISAPI Rewrite .
ISAPI Rewrite is a powerful URL manipulation engine based on regular expressions. It acts mostly like Apache's mod_Rewrite, but is designed specifically for Microsoft's Internet Information Server (IIS). ISAPI Rewrite is an ISAPI filter written in pure C/C++ so it is extremely fast. ISAPI_Rewrite gives you the freedom to go beyond the standard URL schemes and develop your own scheme.
Eu usei para diferentes propósitos em nossos servidores e funcionou muito bem. Procure por "Proxying". Aqui está a documentação da Regra RewriteProxy .
Editar:
Você poderia usar essas regras
RewriteCond %{HTTP_HOST} ^mydomain.com$
RewriteProxy ^(.*) http://local-server-ip/appdir-for-domain/$1 [H,A,L]
RewriteCond %{HTTP_HOST} ^myotherdomain.com$
RewriteProxy ^(.*) http://local-server-ip/appdir-for-otherdomain/$1 [H,A,L]
ou algo assim:
RewriteCond %{HTTP_HOST} ^mydomain.com$
RewriteProxy ^(.*) http://mydomain.com.intranet$1 [H,A,L]
RewriteCond %{HTTP_HOST} ^myotherdomain.com$
RewriteProxy ^(.*) http://myotherdomain.com.intranet$1 [H,A,L]