I had a Lucene computed index field which was indexing item URLs on a multi site environment. The URLs being returned by LinkManager.GetItemUrl were coming back in an unexpected format: ://myUrl instead of http://myUrl. This was because the scheme element was missing off of the site definiton:
<site hostName="MySite" name="mysite"scheme="http" ... />Aka the scheme element needs to be present otherwise the link manager will not include the protocol.