Try Beyond CompareBeyond Compare. It is very flexible, it supports many many formats and will now compare 3 files.
http://www.scootersoftware.com/
EDIT
You can alias a section from one file to one in another file even when the automatic scanner rejects the similarity. That is, you can force it to diff the sections you want to compare.
Text files can be viewed and edited with syntax highlighting and comparison rules tweaked specifically for documents, source code, and HTML.