I am still learning (how much I don't know) lots about under the covers drupal...

Drupal Development email list archive has great insite on how things got to where they are..

api.drupal.org/api/5 is the source for the source code comments - some are very light on actually how to do things ... but it usually links to somewhere the function is used in core. ( just not contrib modules)

Drupal Handbooks great for searching but .... hard to figure out what is for what version .. but continues to improve .... I know I should try to help out and not whine..