How do I use S/MIME, PGP or GnuPG to send and receive signed or encrypted messages?
To use S/MIME, go to Tools > Account Settings… > account name > Security (Edit > Account Settings… on Linux). You can set which certificates to use with each account for digital signing and/or encryption. Hooks to PGP or GnuPG are not included in Thunderbird, but are under development at Enigmail.