I was recently reminded of a problem I had previously experienced but subsequently forgotten with regard to MOSS content crawling.
In this particular instance I was using a custom protocol handler but I believe this issue will apply to the OOTB MOSS Search functionality as well. I was attempting to crawl a file share using a custom protocol handler and kept receiving a myriad of misleading error messages in the application event log, including:
The specified address was excluded from the index. The crawl rules may have to be modified to include this address. (0x80040d07)
as well as:
The update cannot be started because all of the content sources were excluded by crawl rules, or removed from the index configuration.
It turns out that if the Office SharePoint Server Search windows service credentials are changed this corrupts the password of the default content access account being used by the SharePoint search SSP.
To resolve this issue I went to SharePoint Central Administration > Search SSP (i.e. SharedServices1 etc) > Search administration > Default content access account and re-entered the crawling account password.
After doing this everything was peachy, no more errors in the event log.