Most notoriously, the port featured a different storyline, extra weapons (flamethrower and rocket launcher), differently laid out levels and most importantly - heavy censorship.
Adolf Hitler is now Staatmeister and all Nazi imagery have been removed from the game. Blood and gore has likewise been more or less vetoed. The storylines from original Wolfenstein 3D and Spear of Destiny are somewhat entertwined, with featured bosses being the Grösse Brothers Hans and Trans, Doctor Schabbs, the Death Knight (using the moniker Black Knight) and the Ubermutant, in addition to the aforementioned Staatmeister.
With these limitations, in addition to the gameplay which features a very short-sighted overlook (graphics looks detailed only if the player is close to them) and a soundtrack which has likewise gone through a set of limitations, the SNES port of Wolfenstein 3D has a devoted following, and numerous resources of the port have featured in many mods, most of all the weapons.