Just wondering! [this list is also a more general list of relevant 501(c)(3) organizations) that’s more useful for people who want to donate extra funds to - eg I was once gifted $50 to donate to any longevity org several years ago and I very predictably gifted it to SENS]
http://survivalandflourishing.fund/
Related to SFF’s Speculation Grants Program | Survival and Flourishing.Fund (SFF) (see the grant they awarded to Elizabeth von Nostrad for example)
Zvi’s Thoughts on the Survival and Flourishing Fund (SFF) - LessWrong [this is extremely good advice on how to apply to these]
Foresight Institute is one (The Foresight Institute - Nonprofit Explorer - ProPublica ), as is the Mormon Transhumanism Association. Of all of the organizations, Foresight is definitely the most effective/visible (+highest local delta) and attracts the most important individuals.
Also the Calorie Restriction Society - Calorie Restriction Society - Nonprofit Explorer - ProPublica . Last updated in 2015. People really really “hate” on CR though [I only use small “h” on hate because at least it does not make them want to cancel you, which is a qualitatively different kind of hate]
There is also Longevity Research Institute - Nonprofit Explorer - ProPublica (longevity research institute), which has not operated in a while.
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Examples of huge nonprofits (not directly longevity): American Heart Association Inc - Nonprofit Explorer - ProPublica (AHA), American Lung Association - Nonprofit Explorer - ProPublica, Dole Nutrition Institute - Nonprofit Explorer - ProPublica, The Asperger Autism Network Inc - Nonprofit Explorer - ProPublica
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I can’t find any anti-microplastic or environmental health organizations (yet) even though these are also relevant
Alliance For Self Directed Education - Nonprofit Explorer - ProPublica (alliance for self-directed education) is surprisingly value-aligned (longevity is still contrarian and you need more unschooling/self-directed/contrairan education in order to get people into contrarian fields without having to unlearn toxic former habits like death’ism) - an “unschooling first” approach to life breeds more people interested in lifelong longevity. Autism/neurodivergence non-profits might be slightly relevant because the best sources of orthogonal innovation tend to come from autists/neurodivergents who often need extra support (esp as they are often non-responsive to traditional sources of income). I don’t know of a neurodivergence institution that broadly supports innovation well, however (not even the pro-unschooling orgs).
[there are orgs that also more broadly increase the freedom/agency of young people and these are important for generating divergent viewpoints - these are Atlas Fellowship/Thiel Fellowship/1517 fund/HackClub - but I don’t know if these are 501(c)3]. Also for scientific research, agency-increasing organizations include Arcadia (https://www.arcadiascience.com/ ), NewScience. There are also loads of FROs (see Milan Cvitkovic, Sabrina Singh, Ales Flidr) but this then goes off-topic [I’m already off-topic enough for promoting unschooling/neurodiversity here but they are relevant to the “upstream factors” behind longevity 
].
[some like Rochelle Shen/Shagun/Mina Fahmi have created lists of early-stage startup neurotech orgs but this is getting to the realm of not-being-as-relevant.]