Mindgames: Fool's Mate is a standalone novella. The Skinner is set in the same universe as the quintology but a few hundred years in the future and Voyage of the Sable Keech is a sequel to it. Hilldiggers is set even further in the future and Prador Moon is way in the past (but our future) set during the Prador War mentioned in the other books. Africa Zero (two novellas) is standalone as are The Parasite and Cowl (the latter being a time-travel novel). The Engineer ReConditioned is a novella and collection of short stories, some of which are set in the Polity universe and are precursors to the books.

Obviously: clear as mud...