Is there anyway to make a specific warning not trigger a non-zero return code?

The warning I would mostly like this for is "no glyphs for character'

Also is there a different error code for if or not output is a valid PDF (ie. there were only warnings but not errors)?

For that level of integration you might want to actually read the log output from Prince, similar to what our wrapper libraries do. Are you using one of the wrapper libraries?

At the moment I am using perl by parsing the verbose output, which is difficult.

I just checked the wrappers and I didn't realise that there was a --server option (its not in http://www.princexml.com/doc/command-line/?)

That makes it much easier

Also what does --silent do? Hold back everything except fin?

Yes. We are currently modifying the logging system, and the new options will be documented. But the old options will also stick around for a while, for backwards compatibility.