Cryptography

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/

Network Security Services for Java (JSS)
Libraries used internally by Netscape and iPlanet products that do crypto in Java. [Mozilla]
http://www.mozilla.org/projects/security/pki/jss/

The PC1 Encryption Algorithm
The source code of the 128-bit PC1 cipher algorithm in Java.
http://membres.lycos.fr/pc1/

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