See also:
FlexiCrypt Crypto toolkit based on FlexiProvider. http://developer.gauner.org/flexicrypt/
FlexiProvider An open source cryptographic class library for the JCA/JCE architecture. [Open Source with registration] http://flexiprovider.cdc.informatik.tu-darmstadt.de/
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] http://www.christopher-wolf.de/hfe/
IAIK Java Crypto Products Provides a set of Java-based crypto products. Java implementation TLS, SSLv3 and SSLv2(client side), S/MIMEv2. [Commercial] http://jce.iaik.tugraz.at/
Java Cryptography Extension (JCE) Provides framework and implementations for encryption, key generation and key agreement, and Message Authentication Code (MAC) algorithms. http://java.sun.com/products/jce/
JSDSI Reimplemented the Java SDSI (Simple Distributed Security Infrastructure) API. [Open source, MIT License] http://jsdsi.sourceforge.net/
J2SSH Maverick A fully featured SSH2 library. By 3SP LTD. [Commercial] http://3sp.com/showMaverick.do
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] http://www.bouncycastle.org/
QuartzLight in Java Public key signature system QuartzLight [Open Source, GPL]. http://www.christopher-wolf.de/ql/
RSA BSAFE Toolkits for SSL, general cryptography, and PKI. [Commercial] http://www.rsa.com/node.aspx?id=1204