An informal list supplied by current graduate students: 

AAAS https://www.amacad.org/about/fellowships

ACLS https://www.acls.org/Programs

American Antiquarian Society https://www.americanantiquarian.org/fellowships

CLIR Fellowships https://www.clir.org/fellowships/

Colby College Postdoctoral Fellowship in STS

Columbia Center for Science and Society https://scienceandsociety.columbia.edu/node/36

Columbia Society of Fellows http://societyoffellows.columbia.edu/fellowship/

Cornell Society for the Humanities https://societyhumanities.as.cornell.edu

Dartmouth Society of Fellows https://www.dartmouth.edu/sof/fellowships/postdoc.html

Emory University Race and Human Difference::http://jamesweldonjohnson.emory.edu/home/fellowship/apply.html

European University Institute Post Doctoral Fellowships https://www.eui.eu/ProgrammesAndFellowships/Fellowships

Gerda Henkel Foundation https://www.gerda-henkel-stiftung.de/application_research-scholarships

Harvard Academy of International and Area Studies: http://academy.wcfia.harvard.edu

Harvard Society of Fellows: https://socfell.fas.harvard.edu/nomination-procedure

Herzog August Bibliothek  http://www.hab.de/en/home/research/fellowships/post-doctoral-fellowships...

Jackman Humanities Institute University of Toronoto https://humanities.utoronto.ca/funding

Katz Center for Advanced Judaic Studies https://katz.sas.upenn.edu/fellowships/fellowship-program

Max Weber Institute https://www.maxweberstiftung.de/en/startseite.html

McGill Mellon Post-doctoral Fellows: https://www.mcgill.ca/arts/research/postdocs/mellon-postdoctoral-fellows 

McNeil Center for Early American Studies http://www.mceas.org/postdoctoralfellowships.shtml

Michigan Society of Fellows: http://societyoffellows.umich.edu/the-fellowship/application-guidelines/

MIT Mellon Post-doc: http://shass.mit.edu/graduate/mellon_postdoctoral_fellowship

National Humanities Center https://nationalhumanitiescenter.org/become-a-fellow/

Newberry Library http://www.newberry.org/long-term-fellowships

Northwestern Science in Human Culture: http://www.shc.northwestern.edu/post-doctoral/application.html 

Penn Biomedical Ethics: http://medicalethics.med.upenn.edu/education/penn-fellowship-in-advanced...

Penn State Critical Information Post-doc: http://chi.la.psu.edu/fellowships

Presidential Scholars in Society and Neuroscience: http://presidentialscholars.columbia.edu/society_neuroscience_scholars/

Princeton Society of Fellows https://sf.princeton.edu

Science History Institute https://www.sciencehistory.org/fellowships

SSRC https://www.ssrc.org/fellowships/

Stanford Clayman Institute Post-Doctoral Fellowships https://gender.stanford.edu/join-us/fellowships/postdoctoral-research-fe...

UC Berkeley https://spo.berkeley.edu/fund/hpostdoc.html

University of Chicago Society of Fellows

Volkswagon Foundation https://www.volkswagenstiftung.de/en/funding

Wenner-Gren Foundation http://www.wennergren.org/grantprograms/Grants%20for%20Post-Ph.D.%20Scho...

Wesleyan Center for the Humanities https://www.wesleyan.edu/humanities/fellowships/index.html

Yale University, Post-Doctoral Fellowship in Environmental History and Humanities: https://apply.interfolio.com/59960

 

http://www.frias.uni-freiburg.de/en/funding-programmes

https://www.iash.ed.ac.uk/fellowship-programmes

https://www.postdocs.ubc.ca/award/killam-postdoctoral-research-fellowship

http://www.kings.cam.ac.uk/research/junior-research-fellowships.html

https://www.trin.cam.ac.uk/applying/jrf/

https://www.chu.cam.ac.uk/about/master-fellows/junior-research-fellowshi...

https://pages.wustl.edu/mii

http://societyoffellows.umich.edu/

https://www.nypl.org/help/about-nypl/fellowships-institutes/center-for-s...

https://www.hs.ias.edu/mem_announcement

http://www.americanantiquarian.org/longterm.htm

https://www.bgc.bard.edu/bgc-research-fellowship

https://www.ghi-dc.org/fellowships-programs.html?L=0

https://www.nsf.gov/pubs/2015/nsf15506/nsf15506.htm

http://class.cohass.ntu.edu.sg/Research/Pages/Postdoctoral-Fellowship-Op...

http://www.dfg.de/en/research_funding/