Working on a new intranet site for a client I was puzzled when only the homepage of the root site collection would appear in search results. We have site collections on managed paths below the root site and those weren't showing either. Crawls were running but the crawl log showed "Some parts of this document cannot be accessed". I checked the sharepoint logs and the windows event log, then googled away as usual but there weren't really any further clues, everything seemed to be as it should be.
I tried a reset all content on the search index and this made no difference, next up I tried a new content source as I had I noticed some blogs and forums had mentioned an error meessage saying
The start address http://intranet/sites/sitename is not valid for this content source type.
So I tried creating a content source of SharePoint Sites pointing at the site collections on managed paths, these also gave this message - Ah!, progress I thought as it gave another clue. But alas, no further clues were to be found. In the absence of any further hits on google revealing an insight that would solve it. I tried a restart on the Search Service and the Timer service followed by a full crawl. And straight away the crawl log started to give me more than just one hit on the new location, by the end of the crawl there were all the results I had been expecting first time round.
The only thing I can think confused it was that we recreated the site collections several times during deployment and that caused it to get confused.
I hope that little gem helps you out of a spot if search isn't bringing back the results you're expecting.