Being a fan of db4os easy-of-use, I like to guide your attention to this blog, giving a nice overview about the various approaches for queries, esp. the native queries.
Since I've been investigating on persistence recently, I found that performance might be an issue, esp. when thinking about embedded databases.
So I organized a race (very obviously inspired by db4o's Formula1 tutorial) and put the results online in form of the SourceForge project PolePosition
Currently I lined up these database systems for some training laps:
Apache Derby (...
Can unstructured information + cool technology do the job?
short review of a lightweight persistence solution