We are developing XML over HTTP service and we need a way to document the XML interface. Our supported XMLs generally are subsets of some industry standard XML API, which unfortunately lacks any good documentation. It has XSDs though with some annotations, so we use this go generate the initial documentation and then remove the unsupported parts and refine the result. But this process is tedious and the results aren't at all great.

Any suggestion about documentation formats and tools?

I prefer to have HTML output and possibly more, e.g. PDF. Oh, and we are mixed Linux and Windows shop, so the tools should work well on both.