There’s a great article that can be found here listing the different types of contentclass that can be removed from SharePoint scopes. Basically adding these with exclude option will stop such things as lists appearing in search results.
Simply modify the search scopes in the SSP by clicking new rule. Note that on this demo I am using ‘all sites’ scope (I’m being lazy) however I would advise for live environments creating a separate scope and editing the properties of this.
On the new rule select the following properties
and click ok!
This will now remove document library’s from appearing in search results but still display documents within – no re-crawl is required as this configuration is applied at the scope level and not at the content source level.
Further contentclass properties can be found on Jeremy Jameson’s blog.