Pooka supports both S/MIME and OpenPGP, the two most common protocols for email encryption. Both are supported using the JavaMail-Crypto library from SourceForge, which provides a simple, generic encryption integration with JavaMail. The BouncyCastle encryption library is used as a backend for S/MIME encryption, while the Cryptix library is used for OpenPGP.
Using each of these protocols, users can sign outgoing emails and read encrypted emails using their private keys, and encrypt messages and verify signed messages using other people's public keys.
Note that you need Sun's Unlimited Strength JCE Policy Files in order to run this encryption library. You can download those from Sun (link is at the bottom of that page); follow the instructions there for installing the policy files in your JRE.
Pooka does not yet have the ability to generate new public/private keys for S/MIME or OpenPGP, so it is necessary to generate these keys in a third-party application. Once you have set these up, you can go into the Configuration->Encryption Configuration menu. There you can configure the location of the keystore files you have created which contain your public and private keys.