First off: Fantastic program! Use it and never looked back.
My suggestion: make StokeIt recognize which window is under the mouse cursor when drawing (start click), then send commands to that window.
Reason: I use Q-Dir (a quad-window file manager) and use StrokeIt to move forward/backwards though the directories. The problem is if you want to do that through a particular window, that window first needs to be in foreground (focussed), not background.
eg: say if one of the top window is in the foreground, and I draw back/forward on one of the bottom windows... it's the top focussed window that moves. Slightly annoying!
It would be convenient if StrokeIt knew which window you are drawing on then work with that window, foreground or background.
Cheers and Thank You for your work.