Vanilla Cave Story has some extra functionality if certain empty files without file extension are present in the same directory as the EXE.
s_reverse- Swaps the weapon switch keys.
mute- Unhides a context menu which opens a window for muting different Organya channels.
fps- Enables a Framerate counter.
These options are not present in vanilla, but were added in ModCS.
debug- Enables the Debug Console and unhides the "Debug Save" option.
2x- Multiplies all drawing Rects by two, allowing you to use sprites double the size of the vanilla game's.
ntsc- Makes the limit of the game's framerate 60 FPS.