Where I need markup, I've been sticking to HTML or LaTeX syntax for the most part.

Partly because I hate Markdown due to its inconsistent syntax (that's my personal opinion), but also because it feels like a fad of recent years, much like a successor of the MediaWiki fad and the BBcode fad. I feel like in another 2 or 3 years someone will invent Markleft or Markright or Visual Markdown#.NET 2.0 or Dustindown that's 10 times better than Markdown, and then I'll have to switch everything over yet again.

HTML and LaTeX on the other hand, aren't dying any time soon due to their extensive deployment, and I'm confident that my syntax will be renderable for at least another 10 years or more.