Note - this is the small 3 axis indicator in the lower left corner of your viewport, normally dark grey.
Make sure all instances of Rhino are closed first, then run Regedit
Edit the following registry key:
HKEY_CURRENT_USER\
Software\McNeel\Rhinoceros\3.0\Scheme:Default\Options\AppearanceSettings
The last 3 keys are the icon colours. Enter an RGB value
(for example 0,255,0 for green or 255,255,0 for yellow)
These settings are now mostly accessible directly from the Rhino interface. The icon colors are adjustable individually for each display mode (there is no global setting).
In Options > Appearance > Advanced Settings, for each display mode (Wireframe, Shaded, etc.), expand the tree and go to the Grid section. Under "World Axes Settings", you will find three choices - "Use application settings" will use the standard gray, or you can set them to be the same as the normal CPlane X,Y,Z axis colors, or specify another custom color scheme. You will need to do this for ALL display modes you want to customize.
If you want to change the default "application settings" dark gray, follow the same procedure for editing the registry as above for Rhino 3.0 - just edit the key Software\McNeel\Rhinoceros\4.0\Scheme:Default\Options\AppearanceSettings
Ensure you have closed all instances of Rhino before making these changes.
Edit the following registry key:
HKEY_CURRENT_USER\
Software\McNeel\Rhinoceros\3.0(or 4.0)\Scheme:Default\Options\MouseSettings
middle_mouse_dblclk_remap 3
middle_mouse_down_remap 3
middle_mouse_move_remap 3
middle_mouse_up_remap 3
right_mouse_dblclk_remap 2
right_mouse_down_remap 2
right_mouse_move_remap 2
right_mouse_up_remap 2
middle_mouse_dblclk_remap 2
middle_mouse_down_remap 2
middle_mouse_move_remap 2
middle_mouse_up_remap 2
right_mouse_dblclk_remap 3
right_mouse_down_remap 3
right_mouse_move_remap 3
right_mouse_up_remap 3
And you’re done!