Having a iPhone, iPad, and magic pad on my iMac I have become to prefer natural scrolling when using any trackpad like device.

To get it to work on my little Acer running Ubuntu I need to add a .Xmodmap file to my home folder with the following line

pointer= 1 2 3 5 4 7 6 8 9 10 11 12

So what is this doing?

The numbers represent the buttons on your mouse.

1 left button
2 right button
3 middle button
4 scroll up
5 scroll down
6 scroll left
7 scroll right

So as you can see we have basically just reassigned the scroll button (wheel) assignments.

There are lots of other things you can modify with the .Xmodmap file. Check out the documentation for all the details.