Rik at The Click Heard Round The World has put together a list of groupings of non-profit organizations with a presence in SL.

Rik notes that non-profit activity in SL is ever-evolving, as one-off events are always occurring and orgs just catching onto SL begin to set up islands to outreach to the metaverse. He also links to umbrellas such as Commonwealth Sim, the New Media Consortium, and others.