Short version
We need a Maven Doxia alternative being able to generate good looking PDFs (at least code snippets should be properly indented and have configurable font size). Maven guys proposed maven-pdf-plugin in DOXIA-419, but it has same problems. Aforementioned DOXIA-419 has details on difficulties we've experienced with Doxia.
Detailed version
We develop a BIG product providing Java/C/C++/C#/etc API. Tens of client-customized branches are maintained/developed simultaneously. We need a tool to facilitate automatic document generation meeting these requirements:
Include arbitrary snippets from Java/XML/etc samples. Confluence Snippet Plugin is a good example of this feature.
Generate good looking printable documents (e.g. PDF).
Generate online documents having clickable cross-references etc (e.g. HTML).
Unattended mode (e.g. should be easy to run document generation process from Ant script).
Documentation source content (from which PDFs/etc are later generated) should be kept in a human-readable easy-to-diff format.
Documentation source content should be kept in separate files (not Java sources).
Support (Java/xml/etc) syntax highlighting.
UPDATE: 8. Windows OS compatibility.