One of the biggest offenders is scipy, Python's very good and very widely used statistical computing library. The soon-to-be-released scipy 0.9.0 does support Python 3 [0], but Python 3 was released in 2008, so it's taken quite a while.
Another big problem has been with web applications. Python has WSGI, a standard interface for implementing webapps that allows you to use a lot of different frameworks with a lot of different servers. (Similarly to Ruby's Rack and Java's servelets.) However, the WSGI standard for Python 3 (which has to be changed because the existing specification has encoding-related issues in Python 3) has only just been finalized as PEP 3333 [1].
[0] http://projects.scipy.org/scipy/roadmap#python-3 [1] http://www.python.org/dev/peps/pep-3333/