There is a project, POI, to read and write DOC and XLS files with Java.
There is also an existing package, iText, to write _new_ PDFs with Java.
However, I'm not aware of any way to _CONVERT_ DOC or XLS files to PDF
directly. Naturally, that doesn't mean that there is no way to convert them,
just that I don't know of any such tool.

You can find the POI project here: http://jakarta.apache.org/poi/. You'll
find that the ability to write XLS files is apparently fairly mature but
that the ability to write DOC files is still fairly primitive.

You can find the iText project here: http://www.lowagie.com/iText/.

Perhaps you could use POI to read your DOC and XLS files into a Java
program, extracting the relevant pieces of text, then writing them out again
in PDF format. I've never used POI, even for the most trivial of documents,
but I have been quite happy with iText so this approach _might_ work if POI
will co-operate.....

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Rhino

If you can get the data out of the DOC files,
the Apache FOP project can convert XSL-FO documents to PDF

http://xmlgraphics.apache.org/fop/