[eluser]darkhouse[/eluser]
This .htaccess works great for me, you don't have to worry about folders or special files or anything:
Options +FollowSymlinks
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.+)$ index.php?/$1 [QSA]