db4o  
   Object database in Java for Java. [Free for non-commercial]
   http://www.db4o.com/

XL2  
   OODBMS that uses persistent references to scale Java Object Serialization. [Open Source, GPL]
   http://www.xl2.net/

SOD  
   Alpha-quality object-oriented database providing ODMG-conforming Java and C++ language bindings, for Windows and Linux. [Free for personal use]
   http://www.tneumann.de/sod/index.html

JYD Object Database  
   Pure object DBMS written entirely in Java. Multi-user with client-server support and garbage collection. [Commercial]
   http://www.jyd.com/

PJODe - ODBMS for Java  
   Small footprint ODBMS for Java, written in Java. Simple API and customizable query interface. [Free for non-commercial]
   http://www.linxpda.com/

CudenDB  
   Java Object Database. It have simple interface like: 'store', 'get', 'delete', and 'query'. BTree algorithm is used for storing and searching. Indexes to allow for fast search. Transactions: 'beginTransactions', 'endTransactions', 'commit', and 'rollback
   http://www.geocities.com/cudendb/

Jeevan  
   100% pure Java Object Oriented Database, with a simple API and no schema definition language. [Commercial]
   http://www.w3apps.com/index.jsp

FastObjects j2  
   A pure Java object database (ODBMS) component embedded into Java applications to provide object persistence. The j2 OODB is compliant with JDO and is designed for use in embedded systems.
   http://www.fastobjects.com/us/FastObjects_PandS_j2.asp

ObjectStore  
   A complex data management and real-time event processing application for Java and C++ applications.
   http://www.objectstore.com/products/objectstore/

Sieben Geisslein  
   An object store implemented in Java. [Open Source, BSD style]
   http://siebeng.sourceforge.net/