Donors: Organizations don’t have to disclose names of donors/grantors on 990s, they must disclose who they grant funds to. You can match donors with orgs donated to using CitizenAudit.
Follow the Money - political and corporate connections to organizations
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LittleSis
Watchdog network connecting the dots between the world's most powerful people and organizations.
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Nonprofit Data Search
From opensecrets.org, tracks political activities, financial links, and hidden networks of nonprofit groups
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Conservative Transparency
Interactive database that tracks the flow of money among conservative donors, organizations, and candidates.
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Retraction Watch
Tracks retractions of scholarly articles