This is a guide that I wrote to improve the default security of my website https://fortran.io , which has a certificate from LetsEncrypt. I'm choosing to improve HTTPS security and transparency without consideration for legacy browser support.
WARNING: if you mess up settings, lose your certificates, or decide to no longer maintain HTTPS certs, these steps can and will make your domain inaccessible.
I would recommend these steps only if you have a specific need for information security, privacy, and trust with your users, and/or maintain a separate secure.example.com domain which won't mess up your main site. If you've been thinking about hosting a site on Tor, then this might be a good option, too.