Some of these that I believe are at least partially documented, so could be added to the index. But the index for these is not very good anyway, because they are listed in a funny (ASCII-betical?) order in a special section called “symbols”, rather than alphabetically as you would expect. But that would be a separate issue.

Potential index entries:

builtins.__build_class__() → https://docs.python.org/dev/library/dis.html#opcode-LOAD_BUILD_CLASS
__builtins__ global variable → https://docs.python.org/dev/reference/executionmodel.html#naming-and-binding
__conform__() method → https://docs.python.org/dev/library/sqlite3.html#letting-your-object-adapt-itself
__isabstractmethod__ → https://docs.python.org/dev/library/abc.html#abc.abstractmethod
Enum.__members__ → https://docs.python.org/dev/library/enum.html#iteration
__objclass__ → https://docs.python.org/dev/reference/datamodel.html#implementing-descriptors
type.__prepare__ → https://docs.python.org/dev/reference/datamodel.html#preparing-the-class-namespace
__pycache__/ directory → https://docs.python.org/dev/tutorial/modules.html#compiled-python-files
object.__signature__ → https://docs.python.org/dev/library/inspect.html#inspect.unwrap
object.__sizeof__() → https://docs.python.org/dev/library/sys.html#sys.getsizeof
module.__test__ → https://docs.python.org/dev/library/doctest.html#which-docstrings-are-examined
Real.__trunc__ → https://docs.python.org/dev/library/math.html#math.trunc
module.__warningregistry__ → https://docs.python.org/dev/library/warnings.html#warnings.warn_explicit
object.__weakref__ → https://docs.python.org/dev/c-api/typeobj.html#c.PyTypeObject.tp_weaklistoffset

Others that are referenced by the documentation, but not explained anywhere that I can tell:

* module.__version__, referenced as an attribute in a few modules and also in sample code
* __getformat__(), __setformat__(), __getinitargs__() methods, referenced in “unittest.mock” documentation

Regarding __base__, I always assumed this was a leftover from Python 2 from some time before multiple inheritance, so maybe __bases__ could be used instead now (unless testing backwards compatibility).