Turns out the thieves first hack your web browser (through the usual means) and then alter the web page of your bank to display instructions to install a "security" app on your smartphone (MITB attack). So then they have access to both factors and you're boned. Google "Eurograbber" to find out more.
What I find kind of scary is the usual caution is likely to fail. After all, this is the correct URL and the correct SSL cert, so if the fake visuals are well produced it will appear completely legit.
I suppose one approach is to make sure you always logon with a clean browser, so I was thinking of a portable VirtualBox with a copy of Linux used solely for the purpose of online banking. I could even hand out keys to my friends.
Do you think this would be effective? And what precautions do you take with online banking?