Has anyone found anything that has changed in this version yet? One has to assume that something was added, and I can't think of any bugs that would've been fixed... a mystery it is indeed.
According to a translation by Shih Tzu (one of the japanese->english translators for Cave Story), 1.0.0.6 has
* Reduced the CPU load.
* Expanded the 'Troubleshooting' section of the manual.
* Fixed the display of Naoku's picture in the manual.
* Added a sound effect for the Gravekeeper's attack.
* Added an effect for the Behemoth's charge.
* Fixed a bug in the Main Artery stage.
* Fixed a problem regarding processing issues on the title screen only."