According to the Game Releases page on cavestory.org, the Japanese version of Cave Story 3D included extra bonus content.
Cave Story on the Nintendo 3DS (physical release) with new 3D graphics, new or expanded areas, slightly increased difficulty, new item locations, new music remixes and a time attack mode.
Japanese release exclusively contains crossover content from Crazy Climber, Ikki, and Dragon Slayer.
This exclusive content was briefly mentioned in an article by Siliconera.
The Japanese version of Cave Story 3D will have additional content. Nippon Ichi included retro game collaborations with content from Ikki, Dragon Slayer, and Crazy Climber. Right now, Nippon Ichi is keeping the details of these collaborations under wraps.
This content was also mentioned in RedRiderX's Cave Story comparison guide, but once again, no real detail was given.
Numerous easter eggs for old fans of the game and "cross-over content" with nods to Prinny in the western version, and content from Crazy Climber, Ikki, and Dragon Slayer added to the Japanese version
What Japanese exclusive crossover content was included in Cave Story 3D? Was the crossover content significant, or was it limited to minor easter eggs?