Comment 7 for bug 966237

There's a solution for trackpads.

 xinput list-props will give you something like this:
Code:
Device 'SynPS/2 Synaptics TouchPad':
   Device Enabled (133): 1
...
   Synaptics Two-Finger Pressure (269): 282
   Synaptics Two-Finger Width (270): 7
   Synaptics Scrolling Distance (271): 112, 112
   Synaptics Edge Scrolling (272): 0, 0, 0
   Synaptics Two-Finger Scrolling (273): 1, 1
...

The interesting bit being the scrolling distance; replace that with a negative value (with xinput set-int-prop), and you get inverted scrolling.