FlexiCrypt - - Crypto toolkit based on FlexiProvider.
FlexiProvider - - An open source cryptographic class library for the JCA/JCE architecture. [Open Source with registration.
Hidden Field Equations (HFE) in Java - - Java implementation of the public key cryptosystem Hidden Field Equations (HFE). Also includes matrix and finite field operations. [Open source, GPL.
IAIK Java Crypto Products - - Provides a set of Java-based crypto products. Java implementation TLS, SSLv3 and SSLv2(client side), S/MIMEv2. [Commercial.
Java Cryptography Extension (JCE) - - Provides framework and implementations for encryption, key generation and key agreement, and Message Authentication Code (MAC) algorithms.
JSDSI - - Reimplemented the Java SDSI (Simple Distributed Security Infrastructure) API. [Open source, MIT License.
J2SSH Maverick - - A fully featured SSH2 library. By 3SP LTD. [Commercial.
Legion of The Bouncy Castle - - Provides open source implentations of the Java Cryptography Extension 1.2.1, and a lightweight Java Cryptography API for the J2ME, and the JDK. [Open Source.