Jinja, the template engine used for the default HTML templates, is now no longer shipped with Sphinx. If it is not installed automatically for you (it is now listed as a dependency in setup.py), install it manually from PyPI. This will also be needed if you’re using Sphinx from a SVN checkout; in that case please also remove the sphinx/jinja directory that may be left over from old revisions.
The clumsy handling of the index.html template was removed. The config value html_index is gone, and html_additional_pages should be used instead. If you need it, the old index.html template is still there, called defindex.html, and you can port your html_index template, using Jinja inheritance, by changing your template:
{% extends "defindex.html" %}
{% block tables %}
... old html_index template content ...
{% endblock %}
and putting 'index': name of your template in html_additional_pages.
In the layout template, redundant blocks were removed; you should use Jinja’s standard {{ super() }} mechanism instead, as explained in the (newly written) templating docs.
Thanks to Jacob Kaplan-Moss, Talin, Jeroen Ruigrok van der Werven and Sebastian Wiesner for suggestions.