UPDATE:The aricle is old.Links are not available anymore.
Some time ago I looked for DotNetNuke 4.0 API Reference Help File . For some time online help and offline version was available at beta.dnndn.com, but not anymore.
in comments pointed to http://classbrowser.subzero-solutions.net/home.aspx
Also there is no description for many methods (and even classes). It will be good if DNN core team will improve descriptions of the classes and methods.
I understand, that it is a big and quite boring task.
To give community a chance to improve the documentation it could be possible to store the references as wiki and everyone could comment about individual topics. Alternatively each help topic can be attached to a thread on discussion forum.