I think the extension point for your bug tracker syntax would be bogus URL schemes, e.g. [App crashes](bug://CM-2345). These could be handled easily by either a pre-processor or a post-processor or by a custom plugin to your CM parser. I’m not quite sure how I would like Discourse to extend the existing quote syntax using the > line prefix, maybe something like this:
> Currently the focus is on completing the core spec,
> with extensions coming later
-- [chrisalley](topic:1872#2)
It wouldn’t make much sense to limit the discussion here to addons for the reference implementations. Since CM tries to standardize MD it makes sense to also try to match third-party extensions as much as possible, not invent yet another syntax. The extensions in many flavors are actually quite compatible – on the surface at least, they may differ in the ugly details.