Here's a list of the "exclusive" content.
GameStop Pre-Order Bonus - Red Hood story pack
Best Buy Pre-Order Bonus - Waynetech Booster Pack (combat upgrades available earlier) and save $10 on collector's edition strategy guide
Amazon Pre-Order Bonus - 1st Appearance Batman skin
Walmart Pre-Order Bonus - Prototype Batmobile skin and $4.99 VUDU movie credits
Universal Pre-Order Bonus - Harley Quinn story pack
Steam Exclusive - Batman Beyond and The Dark Knight Returns Batman skins
PS4 Exclusive - Scarecrow Nightmare mission, Justice League 3000 and Classic TV Batman skins, and Classic TV Batmobile skin
Limited Edition Exclusives - Batman Memorial statue, steelbook case, issue #0 of Batman: Arkham Knight prequel comic, New 52 skin pack, artbook
Batmobile Edition Exclusives - Fully transformable Batmobile statue/figure, steelbook case, issue #0 of Batman: Arkham Knight prequel comic, New 52 skin pack, artbook
Serious Edition Exclusive (Amazon exclusive) - 1st Appearance Batman skin and Arkham Asylum: A Serious House on Serious Earth hardback 25th anniversary edition
I believe that's everything so far. Note that all of these "exclusives" besides the physical collectors edition items are timed exclusives only, and will eventually be obtainable to all platforms outside of the Season Pass at an unannounced date.