The first way is, as you noted yourself, hardly acceptable as it has countless well-known problems.
The other two have their own problems. For starters, they require manual work when files move (particular bad if you mix it with the application logic, i.e. put it in *.py files instead of leaving it to the computer it runs on) and requires either fixed installation locations (absolute paths) or at least a certain directory structure (relative paths). IMHO, these ways are only acceptable if the applications aren't ever going to move anywhere else. As soon as that becomes required, you should give up and use the existing solution as the one reason not to use it, being overkill for small and local scripts, doesn't apply any more:
Make the common parts, which you apparently already treat as a free-standing library (good!), a fully-fledged project in its own right, with a setup.py that allows installing and adding to PYTHONPATH in a cross-platform way with a single command. You don't need to actually publish it at PyPI, but it makes doing so easier if you should change your mind in the future. Should you do so and also publish some of your projects on PyPI, you also made installing the project in question and its dependencies easier for every potential user.
