What's a good document standard to use programmatically?
Creating XML documents, transforming them to XSL/fo and rendering with Fop or RenderX. If you use  docbook as the primary input, there are toolchains freely available for converting that to PDF, RTF, HTML and so forth.
It is rather quirky to use and not my idea of fun, but is does deliver and can be embedded in an application, AFAICT.
Creating docbook is very straightforward as it has a wide range of semantic tags, table support etc to give a "meaningful" markup which can be reliably formatted. The XSL stylesheets are modular and allow parts to be customized or replaced to generate your own look and feel.
It works well for relatively free flow documents with lots of text.
For filling in the blanks kind of documents, a regular reporting engine may be a better fit, or some straighforward XSL stylesheets spitting out the XSL-fo directly.
I'm writing a program that requires input in the form of a document, it needs to replace a few values, insert a table, and convert it to PDF. It's written in Python + Qt (PyQt). Is there any well known document standard which can be easily used programmatically? It must be cross platform, and preferably open.

I have looked into Microsoft Doc and Docx, which are binary formats and I can't edit them. Python has bindings for it, but they're only on Windows.
Open Office's ODT/ODF is zipped in an xml file, so I can edit that one but there's no command line utilities or any way to programmatically convert the file to a PDF. Open Office provides bindings, but you need to run Open Office from the command line, start a server, etc. And my clients may not have Open Office installed.
RTF is readable from Python, but I couldn't find any way/libraries to convert RTF documents to PDF.

At the moment I'm exporting from Microsoft Word to HTML, replacing the values and using PyQt to convert it to a PDF. However it loses formatting features and looks awful. I'm surprised there isn't a well known library which lets you edit a variety of document formats and convert them into other formats, am I missing something?
Update: Thanks for the advice, I'll have a look at using Latex.
Thanks,
Jackson