Very interesting, I haven't read any of Martin's books, I thought he took inspiration mainly from the War of the Roses, I only saw the tv show, the similarities that struck me while watching that serie:
Two feudal rival houses : starks vs lannisters => atreides vs harkonnen
A charismatic leader and father led to a trap and betrayed early in the story : Ned Stark => Leto Atreides
Some secret societies here and there : Priestess of the Lord of Light => Bene Gesserit and Faceless Men => Bene Tleilax (it's this point, with that "Face Dancer" thing, which confirmed to me the relation between the two universes).
And of course Bran Stark is literally Paul Muad'dib !
I'm sure there's more complete topics about those similitudes, but these are my own conclusions based on the tv serie and not the books.