+ Static websites from any input to html
+ Markdown & TeX & References to pdf for academia
+ Generating manpages for new tools
+ Generating ebooks
... Let's just say I get a bit lost when it isn't available.
Do any of your tools use long options (prefixed with a double dash)? If so, make sure you disable the "smart" extension, otherwise you might end up with en dashes.
For novels, I tend to just use Markdown, as kerning will be done in CSS.
For academics, I use LaTeX and Asciidoc together, but some paragraphs might be inserted in various other formats - whatever is easier. The build tool doesn't care what the format is, it'll take any input pandoc accepts.