Windows have the worst R-value of any part of the home structure. Even with triple-seal low "e" and argon the most you can get is R-5.3, which is almost 6 below a standard wall. The problem with windows is that yo can't get insulation between the panes and still see through.
There is an insulating method used in greenhouses which features foam beads blown between the glass panes. It begins with glass panes placed at least 2.5 inches apart and filled with expanded polystyrene beads. This creates a insulating factor of almost R-11.
A storage unit is placed below the window and there is a pipe that opens between the panes. At night, the blower in the unit is turned on and the beads are blown from the storage tank and fill the window space from the top down. The window is now basically a wall.
In the morning this process is reversed and the motor creates a vacuum going pulling the beads out of the window space making the window clear again.
To stabilize the light in the home on a cold day the window can be filled up halfway or in any amount you want.