Scenario: I have a MOSS 2007 server setup for intra/extranet collaboration using Alternate Access Mapping + 2 Site Collections. One Site Collection for the portal, one for the My Sites. Both set to Basic Authentication only in IIS so extranet users wouldn’t have to type their login as ‘domain\username’.
Problem: The Search Service Crawler Account can only crawl sites that are set to Integrated Windows Authentication. Therefore, crawling won’t occur on the Site Collections using Basic Authentication.
Error Message: Access is denied. Check that the Default Content Access Account has access to this content, or add a crawl rule to crawl this content. (The item was deleted because it was either not found or the crawler was denied access to it.)
Solution: Extend your Site Collections with Integrated Windows Authentication and set the extended Site Collections to be the default websites in Alternate Access Mapping.
References:
http://www.kevincornwell.com/blog/index.php/windows-sharepoint-services-wss-30-search-setup-notes/
The SharePoint Swiss Army Knife 
How does this work with a FILE share on a diff domain? I get the EXACT error. I can map to the remote share using the remote domain account credential but when I add these same credentials into a crawl rule, I still get access denied. Any ideas?