I've released version 1.6 of Lemon, the LEGO® model differ.
Lemon (LEGO® Model Nibbler) is a Java application that compares two LEGO® models laid down in LDRAW or LDD format and lists the parts that are used in one model but not in the other one (and vice versa) as well as the common parts of both models.
It is possible also to check a model against the NXT Retail Kit or the NXT Education Kit.
The new version comprises a new export feature for comparison results (into a text file) as well as numerous bug fixes (in particular for the Java 5/6 version issue).
To install it, just click on the installer link on Lemon's home page (you will need to have Java installed).
If you encounter problems or want to provide feedback, please contact me via my contact page.