What is the difference between "work in" an organisation and "work with"?

Question

I have work experience in local NGOs.
I have work experience with local NGOs.
I have experience working with local NGOs.

Changing the preposition can change the meaning. Is this the case here, or are these sentences effectively identical in meaning?

To me work in suggests as an employee while work with may suggest an external professional relationship. — user66974, Commented Mar 20, 2015 at 9:31
To add to the comment by @Josh61: at a company dinner I introduced my wife to my immediate superior, saying, "This is John - I work for him." John immediately, and kindly, said, "Dave works with me", thus raising my status. But if you're supplying some sort of service for an organization that's not directly paying you, I agree that 'work with' is best. — David Garner, Commented Mar 20, 2015 at 10:38

user21820 · Accepted Answer · 2015-05-02 12:27:48Z

I have work experience in local NGOs.

This refers to your experience of being in the local NGOs for your work. This more or less implies that you were an employee of those NGOs.

I have work experience with local NGOs.

This refers to your experience of doing work together with local NGOs, and it does not matter where you are working and for whom you are working.

I have experience working with local NGOs.

You didn't mention this one, but it is even broader and covers even the case that the local NGOs are subcontractors.

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