This reading list from the Markulla Center on Applied Ethics at Santa Clara University is a great collection of materials covering ethical issues related to digital data. The articles do not specifically focus on civil society per se but they cover a lot of the questions about privacy, data ownership, consent, respect, and security that should be top of mind for foundations and nonprofits.
Here's the link to the reading list:
These issues were covered at our Ethics of Data conference back in September. Great to see attention and interest growing.