Lemon speaks Multipart
Next to LDD and classic LDraw (.ldr) files you can compare also a LEGO® model against the different NXT sets now that is stored as a multipart model in the LDraw .mpd format.
Check out the new version 2.1.0 here and do not hesitate to provide feedback.
Comments
First, I noticed that the part numbers of LDraw files on Peeron (that serve as the source of information for the NXT set definitions) and the ones in the parts lists used by MLCAD and other CAD tools differ sometimes, in particular for newer parts; this will make Lemon showing differences where in fact the part is logically the same (yet, that can't be helped as long as the two sources of part numbers stated above are not completely synchronized).
Secondly, for LDD files, I haven't figured out yet how the retrieve the information about a part's color and description from lxf files (or whether that is possible at all). Hence, for LDD files, that information is not shown in the model table of Lemon. This is not critical in regard to comparison with a NXT set, as part colors and descriptions are not regarded here anyway.