Better integration with search engines. You should be able to search code
and be taken to the line within the JXR version.
Support for alternative source control applications.
Links into similar systems for other languages. It'd be nice to follow links
to native methods into LXR.
Two way linking in JXR. Should be able to see a list of classes dependent on
the current class. Could you display a diagram showing the dependency tree.
Sounds like a job for SVG or maybe VRML ;O).
Allow people to add adhoc links to the left hand tree.