I sticked with Apache Derby for simple desktop application development. Derby (or JavaDB) is becoming part of the JDK, so it might be a good long term bet. The Eclipse plug-in appeared quite useful in this case.
The functionality of the plug-in makes the core jar files available in the project. One could run the ij queries just inside Eclipse console and execute custom scripts using a context menu item available via riht-button-click on the target file.