When I check the option for clean url's in my administration section all links break. Here is my .htaccess file with the default settings in it. There should be a handbook about this that actually contains an anwser!
#
# Apache/PHP/Drupal settings:
#
# Protect files and directories from prying eyes.
Order deny,allow
Deny from all
# Set some options.
Options -Indexes
Options +FollowSymLinks
# Customized error messages.
ErrorDocument 404 /index.php
# 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
php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
# PHP 4, Apache 2
php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
# PHP 5, Apache 1 and 2
php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
# Reduce the time dynamically generated pages are cache-able.