A plugin searched 269 PHP files, of which 167 contained classes and functions, and found 168 classes and 3,856 functions.
WordPress version 3.0 has significant differences from earlier versions, perhaps most importantly, multisite support.
* Note *
The list does not include any found in plugin or theme files as these will differ from blog to blog. Nor does it differentiate between "stand alone" functions and functions that are members of a class, such as the Snoopy functions.
If you know of any Core functions that are not in the list, please leave a comment so I can modify the regex used to find them.