I am running a test version of Drupal on localhost. Under 6.12, clean URLs worked fine. I upgraded to 6.13, without changing my server configuration at all, and clean URLs no longer work.
apachectl -M shows that mod_rewrite is still loaded:
Loaded Modules:
rewrite_module (shared)
Syntax OK
The .htaccess file in /var/www/drupal looks like this:
#===========================================
#
# Apache/PHP/Drupal settings:
#
# Protect files and directories from prying eyes.
Order allow,deny
# Don't show directory listings for URLs which map to a directory.
Options -Indexes
# Follow symbolic links in this directory.
Options +FollowSymLinks
# Make Drupal handle any 404 errors.
ErrorDocument 404 /index.php
# Force simple error message for requests for non-existent favicon.ico.
# There is no end quote below, for compatibility with Apache 1.3.
ErrorDocument 404 "The requested file favicon.ico was not found.
# Set the default handler.
DirectoryIndex index.php
# Override PHP settings. More in sites/default/settings.php
# but the following cannot be changed at runtime.
# PHP 4, Apache 1.