We all know that duplicate content will hamper your search performance, but what about similar theming across sub-domains, international sites, or family sites that have entirely different URLs?
If two sites are related in some way Google may not decipher between them leading to domain conflict.
Have you ever seen a sudden drop for your site in the organic search results then a reappearance several days later?
Or do different landing pages and sub-domains regularly swap places for a search term? If so your site could be affected by site-wide cannibalisation, duplicate theming or semantic flux.