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Another big one: the encodings module API is not documented in the prose docs, and nor is the interface between the default search function and the individual encoding definitions. There's some decent info in help(encoding) though.
The interaction with the import system could also be documented better - you can actually blacklist codecs by manipulating sys.modules and the encodings namespace, and you can search additional locations for codec modules by manipulating encodings.__path__ (even without it being declared as a namespace package)