Newer versions of w3t have an administration command that'll let you run SQL queries directly against your database.
Warning: Do not assume the SQL sample code I'm about to present is in fact correct or nondestructive. I'm not near my documentation so at best there could be syntax errors. At worst I could have the table and field names wrong and, unless you've got rollback enabled, you could break your installation. That said...
If you're current you could go to that page and enter something like "UPDATE w3t_Users SET U_EReplies='On' "
-- David Innes
Disclaimer: I've used the direct SQL feature to change global settings and it worked fine. It's fast and effective. But if you're going to take any of my advice take all of it: practice first on a test installation and database.