Nowadays, this is what I run right after installing Linux systems:
echo "pointer = 1 2 3 5 4 7 6 8 9 10 11 12" > ~/.Xmodmap && xmodmap ~/.Xmodmap
No reboot required. Tested on both my laptop and my desktop machine.
Don’t like it? Reverting is as easy as running the command above again, but swapping the 5 with the 4 and the 7 with the 6.
Long story short, download this, run it and you should be experiencing natural scrolling in its full glory.
If you like it, feel free to stick it in your Startup folder. If you don’t, feel free to press the Delete key. If you don’t feel like running some random .exe, get the AutoHotKey script from here and make your own.
You can also get this behaviour in Linux. Here’s a blog post on that.
P.S.: If you’re worried about my .exe gobbling up your precious system resources, you might want to know that it only eats up 272 kilobytes of RAM on my Vista machine.