I seems that abbreviations and acronyms don't usually require special wiki markup, as they can be automatically detected and marked up by the wiki engine in question.

This is how I've done it in a simple parser for MoinMoin:

 * There is a distinguished page, appropriately titled, containing a list of all abbreviations and acronyms that are expected to be encountered on that particular wiki, together with their descriptions (usually the full name).
 * When this page is saved, an internal representation of it, a hash map, is updated.
 * When a page is parsed, this hash map is used to recognize known abbreviations and mark them up, together with an explanation for them in a title attribute.

The only problem with this approach are abbreviations and acronyms that look like normal words -- depending on their relative rarity as both, they could be escaped in one or the other form. Not sure how.