It would be very helpful to have specific Markdown for creating links directly to the Drupal Reference http://api.drupal.org/api/drupal, especially when you are asking/answering a question that mentions several hooks, or different modules.
I think this could be done as a sitewide thing, where a tag could be used in the bracket syntax.
[proj:views] => Views
[drupal6:hook_menu] => hook_menu()
[drupal7:hook_boot] => hook_boot()
[php:strpos] => strpos()
[actionscript-3:MovieClip] => MovieClip()
Most of the languages I can think of have pretty regular URLs for their online API manuals.