> As for the __main__ dict, perhaps we're missing a decref somewhere.

Actually, it's not surprising. Blob's methods hold a reference to the __main__ globals, and there's still a Blob object alive in encodings.

If you replace the end of your script with the following:

for name, mod in sys.modules.items():
    if name != 'encodings':
        mod.__dict__["__blob__"] = Blob(name)
del name, mod, Blob


then at the end of the shutdown phase, remaining is empty.