Apache Derby
Derby is a Java RDBMS undergoing incubation at Apache Software Foundation. It is a fully functioned standards based JDBC & SQL RDBMS with tables, indexes, views, triggers, sub-queries, procedures, functions, transactions, isolation levels, encryption, etc. Derby is the open sourcing of the IBM Cloudscape technology.

Ashpool
Ashpool is a lightweight XML Database written in Java(tm). It's goal is to use standard SQL92 syntax to query, add, update, and delete XML documents via a JDBC driver. The XML documents must hold to a table like structure. The reason for the table structure restriction is that SQL was designed to query table data not hierarchical data.

Axion
Axion is a small, fast, open source relational database system (RDBMS) supporting SQL and JDBC written in and for the Java programming language.

db4o
db4o is designed to be a simple, easy-to-use, and fast, native object database. Software developers using popular Java and .NET object-oriented frameworks know that using an object oriented databases is a more natural way to get work done. Developers have three ways to storing and retrieving data: relational, non-native object and native object.

Excel JDBC Driver
JDBC Driver for the spreadsheets Excel, StarOffice and OpenOffice. Turn a directory with spreadsheets into a database. xls filenames become database schema's, sheets become tables. Use a rich subset of SQL to create sheets and query sheets. Join sheets, query database data and store it into excel or fill database tables with spreadsheets.

Hypersonic SQL
HSQLDB is the leading SQL relational database engine written in Java. It has a JDBC driver and supports a rich subset of ANSI-92 SQL (BNF tree format) plus SQL 99 and 2003 enhancements. It offers a small (less than 100k in one version), fast database engine which offers both in-memory and disk-based tables. Embedded and server modes are available.

Mckoi SQL Database
Mckoi SQL Database is optimized to run as a client/server database server for multiple clients, however it can also be embedded in an application as a stand-alone database. It is highly multi-threaded and features an extendable object-oriented engine.

One$DB
One$DB is an Open Source version of Daffodil DB, our commercial Java Database. One$DB is a standards based (J2EE-certified, JDBC 3.0 and SQL 99 compliant), platform independent, footprint size database that can be embedded into any application and requires zero or minimal administration.

Quadcap Embeddable Database
QED, the Quadcap Embeddable Database. QED is a fast, small, pure Java, relational database, implementing the SQL 92 standard, with transactions and resilient failure recovery. QED has a novel open source license permitting free use of QED by all and free redistribution in other open source projects.

TinySQL
A very lightweight 100% Java text SQL engine that includes a JDBC driver.