> It appears that a few (1-3) module dicts are not being purged because they 
> have been "orphaned".  (i.e. the module object was garbaged collected before 
> we check the weakref, but the module dict survived.) 

Module globals can be kept alive by any function defined in that module. So if that function is registered eternally in a C static variable, the globals dict will never get collected.

> ./python -v -Xshowrefcount check_purging.py

I always get either:

# remaining {'encodings', '__main__'}
[...]
[24834 refs, 7249 blocks]

or

# remaining {'__main__', 'encodings'}
[...]
[24834 refs, 7249 blocks]

... which seems to hint that it is quite stable actually.
The encodings globals are kept alive because of the codecs registration, I believe.
As for the __main__ dict, perhaps we're missing a decref somewhere.

> Maybe 8 out of 50+ module dicts actually die a natural death by being 
> garbage collected before they are purged.

I get different numbers from you. If I run "./python -v -c pass", most modules in the "wiping" phase are C extension modules, which is expected. Pretty much every pure Python module ends up garbage collected before that.

By the way, please also try issue18608 which will bring an other improvement.