It seems that Aeon has recently updated his nice FAQ of all Dark Messiah secrets to be found in the game. The updated FAQ contains 52 secret and 47 special areas and lists them in the approximate order the player progresses in the game.

Most of these secret areas contain usual stuff like potions, scrolls, weapons and armor however some of them conceal very rare and powerful items like the Earthfire Shield or Souldrinker.

Maybe it's time to replay Dark Messiah and check it all out yourself!