Run all my doctests for all python modules in a folder without seeing failures because of bad imports

You can also create unittests that wrap desired doctests modules, it is a native feature of doctests: http://docs.python.org/2/library/doctest.html#unittest-api.

import unittest
import doctest 
import my_module_with_doctests

def load_tests(loader, tests, ignore):
    tests.addTests(doctest.DocTestSuite(my_module_with_doctests))
    return tests

I think nose is the way. You should either exclude the problematic modules explicitly with -e or catch the missing imports in your code with constructs like this:

try:
    import simplejson as json
except ImportError:
    import json

Update:

Another option is to provide mock replacements for the missing modules. Let's say your code has something like this:

import myfunkymodule

and you're trying run your tests in a system where myfunkymodule is missing. You could create a mock_modules/myfunkymodule.py file with mock implementations of the stuff you need from it (perhaps using MiniMock, which I highly recommend if you are using doctest). You could then run nose like this:

$ PYTHONPATH=path_to/mock_modules nosetests --with-doctest