Here is a list of what I've tried (since software is written in Java, so I tried pure 100% Java solutions):
- Apache Derby (AKA JavaDB)
- Oracle Berkeley DB for Java
- db4o for Java (sort of ZODB for Python, but much better)
- W3C JDBM (ripped off from Jigsaw)
- Some JNI wrappers around GDBM (JDBM and JavaDBM).
If you want objects, use db4o. Very neat database.
If you want embedded SQL, then definitely H2. It is RDBMS from the same author of HSQLDB, just simply faster and better. It has lots of features and very nicely coded. Performance is very high, it supports very large databases, in-memory databases and works in server mode. Footprint is very small and it is 100% pure Java open source software. It also supports ORMs, if you need this thing. But I am not sure how you could install 120M of ORM, then make cumbersome XML mappings, then use weird HQL (as for Hibernate, for example) and stay happy because your database engine footprint is just 500K library... Go real stuff: use plain JDBC with few more codelines and plain SQL that you can write best! It will reduce size of your application hundred times and increase performance at least as twice, no mention perfect maintainability of code, since it is small, easy, simple and very well understandable to anybody.
Apache Derby is the last thing you need. It is actually IBM Cloudscape, if you remember one. Amount of bugs is so big and it coded so nasty, that to open source and change its name is the only way to hope someone will use it. At performance it is slowest and footprint is twice bigger than H2. Additionally, database might get easily corrupted or just suddenly stop booting. Apache Derby is "No Go" for you and you want to avoid it.
Happy New Year! :)
Update: Hooray, I have an alpha version of my "Better Time Machine © :-)" working! And it works really amazing for me: saves disk space, fast, customizable, yet very simple in use. I am going to put it on public domain, once I am sure it will not break your backups. :-)
Some more update: db4o is not 30Mb footprint, sorry. So do not think about it. :-)