Use 3.1
Why?
1) Because as long as everyone is still using 2.6, the libraries will have less reasons to migrate to 3.1. As long as those libraries are not ported to 3.1, you are stuck with the choice of either not using the strengths of 3.1, or only doing the jobs half way by using the hackish solution of using a back-ported feature set. Be a forward thinker and help push Python forward.
2) If you learn and use 3.1 now, you wont have to relearn it later when the mass port is complete. I know some people say you wont have to learn much, but why learn the old crap at all? Python itself is moving towards 3.1, the libraries will move toward 3.1, and it sucks to have to play catch-up and relearn a language you are already using.
3) 3.1 is all around a better language, more stable and more consistent than 2.6... this is normal. The lessons learned from 2.6 were all poured into 3.1 to make it better. It is a process called PROGRESS. This is why nobody still uses Windows 3.1. It is the way things move FORWARD. Why else do you think they went to the trouble of back porting a feature set in the first place?
4) If you are learning Python, and learn 2.6, then by the time you are really comfortable with the language, the ports will be out, and you will have to learn the libraries, and the language all over again. If you start with 3.1, then by the time you are comfortable with the language, the ports will be out, and then you can learn the libraries that you are interested in. It is a smoother process.
5) To be a better developer. If you have to learn and relearn the same things, your understanding will not be very deep. By learning this language, and its libraries only once, you will have more time to work with them rather than relearning syntax. This allows you to understand them better. If you are really missing some pieces by forgoing on the libraries? WRITE THEM. You will probably not need an entire library, and can usually write only those pieces that you need, and develop tools for yourself. This, again, helps you understand the language better, and more deeply.