The architecture is pretty similar to something like WordPress. There will be a qa-plugins folder where you can install plug-ins. A plug-in registers a PHP class to supplement Q2A in a certain way. For the next version four plug-in types will be implemented:
editor for custom content-editing fields (e.g. for WYSIWYG editor)
viewer for rendering content (could use for markdown)
page for custom types of page
login for logging in via other sites (e.g. Facebook Connect)
I know it wasn't such a commonly requested feature but (partly based on your input) it seemed like the most sensible way forwards, both to add new features myself, and to make it easier for other people to extend the system without touching the core.
BTW, plug-ins can also inject a form into the admin interface for their own settings.