Here is a way to do it with .htaccess or httpd.conf:
http://www.askapache.com/htaccess/rewrite-uppercase-lowercase.html
You could write a mysql query that would change all the entries in the database using the Lower() function:
http://dev.mysql.com/doc/refman/5.0/en/string-functions.html#function_lower
To get it to be lowercase from now on automatically:
http://stackoverflow.com/questions/154862/convert-javascript-string-to-be-all-lower-case
Edit /common_files/js/check_clean_url.js
Look at line 69 and find:
to_field.value = from_field.value.replace(/[\&]/g, '-and-').replace(/[^a-zA-Z0-9._-]/g, '-').replace(/[-]+/g, '-').replace(/-$/, '');
Change it to:
to_field.value = from_field.value.replace(/[\&]/g, '-and-').replace(/[^a-zA-Z0-9._-]/g, '-').replace(/[-]+/g, '-').replace(/-$/, '').toLowerCase();;
All we have done is added ".toLowerCase();" to the end of the JavaScript expression. This will work for all new products you create that don't have a clean url value. Or if you remove the Clean URL and make some change to the product name than it will rewrite it for you.