Usually when referencing an external website we use http://…… and
we lose all the security etc. information that comes back from our crawls. (In contrast
to the File://c:/docs/… etc etc)
A handy tip you can do is IF you know the site is a sharepoint site
you can use the SPS moniker so the indexing service uses the Sharepoint
APIs to contact the site as opposed to the http:// protocol
handler.
(1) for SPS v2 use SPS://…..
(2) for SPS v3 use SPS3://….
Enjoy.