You would want to go with 2.6 today.
Why? Because there is no library support for 3.1. We've just finished porting setuptools (under the name Distribute) to Python 3, so hopefully library support for Python 3 will increase dramatically during the next year, but it's not there yet.
And it's not so hard to switch. It's not like it's a whole new language, like some Python critics make it sound like. So if you start with Python 3, it's no disaster either. It's just that it's going to be hard to actually be productive in Python 3 at the moment. So go with 2.6.