Settings - Appearance (Transparency)

Windowed/Fullscreen

If Windowed is selected, you are editing transparency settings available in windowed mode.
If Full screen is selected, you are editing transparency settings available in full screen mode.

None
Alpha and color key
Alpha
Glass
Color key

Specifies transparency type.
Alpha transparency and color key transparency can be used together.
Alpha transparency is the 'real' transparency.
Vista aero glass effect.
Color key transparency allows you to specify a single color that will be made transparent. All window pixels having this color will be transparent and mouse clicks will pass through transparent areas.

Active window

Specifies alpha transparency for while ConsoleZ window is active.

Inactive window

Specifies alpha transparency for while ConsoleZ window is not active.

Key color

Specifies transparency color for 'color key' transparency.