Daffodil DB
- A embeddable, SQL-99 specification compatible, Java-based database engine. [Commercial and open source]
- http://db.daffodilsw.com/

HSQLDB
- RDBMS with JDBC interface, client-server version, query tool, grid, tree, performance test class, servlet, and self-test program. Also supports pure in memory databases. [Open Source, BSD-like]
- http://hsqldb.org/

HyperXtremSQL
- A pure Java RDBMS based on HSQLDB (HypersonicSQL). [Commercial]
- http://www.cluedup.com/hxsql/

SmallSQL
- A desktop SQL database with a small footprint, 100% pure Java, embeddable, SQL 99 conformance, JDBC 3.0 driver. [Open source, GPL]
- http://smallsql.sourceforge.net/

Herodotus DB
- A pure Java RDBMS that supports "Full SQL" level of SQL/92. Using a patented algorithm, all previous states of the database are always directly accessible. [Shareware]
- http://www.herodotus.biz/

PointBase
- Pure Java RDBMS with a JDBC interface including client/server, embedded, and micro (J2ME) products. [Commercial]
- http://www.pointbase.com/

Infinity Database Engine
- An embeddable datastore with data compression, global transactions, integrity preservation, high concurrency, and flexible, extensible data model. [Commercial]
- http://boilerbay.com/infinitydb/

JavaDBF
- A Java library for reading and writing Xbase (dBase/DBF) files. [Open source, LGPL]
- http://sarovar.org/projects/javadbf/

xBaseJ
- A dBASE III & IV compatible Java database. [Commercial]
- http://www.americancoders.com/xBaseJ/

Axion
- A small, fast, SQL and JDBC compliant relational database engine written in and for the Java programming language. [Open source, BSD License]
- http://axion.tigris.org/

Smyle
- (Storage That Makes Your Life Easier) An open source hierchical/relational database, seamlessly integrated with Java. [Open Source, GPL]
- http://www.drjava.de/smyle/

QED
- Small footprint database with transactions, failure recovery, SQL 92 conformance plus many SQL3 features. [Commercial]
- http://www.quadcap.com/home.html

Mckoi SQL Database
- Multi-client / multi-threaded SQL relational database management system written in Java. Includes JDBC 2.0 driver. [Open Source, GPL]
- http://www.mckoi.com/database/

AlgebraDB
- A Java-based, experimental relational database representing functions as infinite tables. [Open Source, LGPL]
- http://algebradb.sourceforge.net/