Dunno if this has been mentioned...
In org.lwjgl.input.Mouse, the "absolute position" returned from getY() isn't consistent with the upper left origin, instead it returns it relative to the lower left. I have to put in (WindowHeight - Mouse.getY()) to get a proper position.
I don't know if it's possible for you guys to do it without also subtracting window height, which would equal no performance benefit. Still, I think it would be better for consistency's sake to match it up with the origin. I think two additional functions in Mouse would work, like getOriginX() (and Y), or maybe getRelativeX() (and Y).