The only "case" that will work is a skin (i.e. Ghost Armor, Zagg Invisible Shield, etc.). Other than that, I am pretty sure more traditional hard shell cases will be too thick.
If you want a case and dock that work together then you need to purchase a combo designed to work together (e.g. Seidio) or a more generic dock (e.g. Mikradle, ezeStand, etc).