The Cutting Room Floor/Mickey Mouse 64

Logo
The logo's letters "64" were less polished and gray in the Japanese version, but in the US, were polished and blue.

Saves
In the Japanese version, there are only 3 save files, but in the US version, there are 4.

Save Icons
Save Icons were added in the US version.

Steamboat Willie
In the Japanese version, after you beat the game, the cinema shows nothing, but in the US, it showed an FMV of Steamboat Willie.

Eyebrows
Mickey had eyebrows in the N64 version that were removed in the GCN version.