Mega Man Zero

Unused Graphics
The sign for basement floor 2 was replaced with a blank blue rectangle. The other signs were removed entirely.

Ciel


A block of unused text can be found if you manage to skip Herculious Anchortus (through cheating or glitching past him) and get to the last Trans Room.

This text can be translated as "It's no use if we don't cancel the protection to go to the city from the Trans Room... But, the password can't be analyzed yet.".

This seems to be from a mission that they scrapped before, or possibly replaced with something else. By the context of the message, it seems that you were to need a pass key or something in order to access Neo Arcadia, rather than Ciel finding it out.

Maha Ganeshariff
This was meant to be Maha Ganeshariff's death line, but in the final game he dies quietly.

Title Theme
The "Rockman Z!" voice clip was removed from all non-Japanese versions of the title track.

Blood Spray


When most enemies are destroyed with a non-Buster weapon in the Japanese version, blood(?) sprays out of them. This was removed from every other version of the game.