Comment 5 for bug 952170

The xorg method doesn't effect any of the newer GTK stuff that using smooth/inertial scrolling. Instead, we should actually invert the values in the synaptics touchpad driver. This ensures that we're also not messing with mouse users.

You can do this with a command like "synclient VertScrollDelta=-n" where -n is the inverse of whatever the value currently is for you. For full effect, you can also invert horizontal scrolling with "synclient HorizScrollDelta=-n"