This is a partial list.

UC Berkeley Library (on behalf of the UC Berkeley campus)
The UCB Library licenses the EZID service for Berkeley researchers. Sponsored accounts:
Open Context Open Context is a free, open access resource for the electronic publication of primary field research from archaeology and related disciplines.
CRCNS.org Collaborative Research in Computational Neuroscience - Data sharing - contains a repository of high-quality experimental data sets that are valuable for testing computational models of the brain and new analysis methods. The data include physiological recordings from sensory and memory systems, as well as eye movement data.
Human Rights Center The Human Rights Center promotes human rights and international justice worldwide and trains the next generation of human rights researchers and advocates.
UC Irvine Libraries (on behalf of the UC Irvine campus)
The UC Irvine Libraries license the EZID service for UC Irvine researchers.
UC San Diego Library (on behalf of the UC San Diego campus)
UC San Diego Research Cyberinfrastructure is the hardware, software, and people that support scientific research. UCSD RCI offers EZID as a component service for researchers.
The UCSD Library licenses the EZID service for UCSD researchers. Sponsored accounts:
OpenTopography: OpenTopography facilitates community access to high-resolution, Earth science-oriented, topography data, and related tools and resources. Support for OpenTopography comes from the National Science Foundation's Earth Sciences: Instrumentation and Facilities Program (EAR/IF) and the Office of Cyberinfrastructure.
UC San Francisco Library and Center for Knowledge Management (on behalf of the UCSF campus)
The mission of the UCSF Library and Center for Knowledge Management is to advance science, foster excellence in teaching and learning, and promote health through the collection, development, organization, and dissemination of the world's health sciences knowledge base. Sponsored accounts:
DataShare, an initiative from the UCSF Clinical and Translational Science Institute.
UC Santa Barbara Libraries (on behalf of the UC Santa Barbara Campus)
The UC Santa Barbara Libraries license the EZID service for UC Santa Barbara researchers. Sponsored accounts:
National Center for Ecological Analysis and Synthesis (NCEAS) NCEAS supports cross-disciplinary research that uses existing data to address major fundamental issues in ecology and allied fields, and encourages the application of science to management and policy.
Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) The Partnership for Interdisciplinary Studies of Coastal Oceans is a long-term ecosystem research and monitoring program.
Bren School of Environmental Science & Management The Bren school integrates science, management, law, economics, and policy as part of an interdisciplinary approach to environmental problem-solving.
UC Santa Cruz Library (on behalf of the UC Santa Cruz campus)
The UCSC University Library holds a growing collection of digitized and "born digital" materials in many formats from the library's archives, including the campus archive, historic maps, faculty papers, the records of the Lick Observatory, and the Grateful Dead Archive.
American Astronomical Society
The American Astronomical Society (AAS) is the major organization of professional astronomers in North America. The mission of the Society is to enhance and share humanity's scientific understanding of the Universe. The AAS publishes two of the major journals in astrophysics.
Centre national de documentation pédagogique
The CRDP (Centre régional de documentation pédagogique) de l'academie d'Aix-Marseille is a public structure member of the Services culture, éditions, ressources pour l'Éducation nationale (SCÉRÉN). The center works with primary and secondary schools providing resources and educational contents. Among its activities: information, publishing, promotion of uses of Information and Communication Technologies, and cultural and artistic activities. The CRDP uses EZID for www.coredu.fr, an online editorial resources catalog for French school establishments.
Cornell Institute for Social and Economic Research
CISER is working on using EZID-generated DOIs for selected studies in its Data Archive.
Consortium on Qualitative Research Methods
The Consortium on Qualitative Research Methods hosts the Institute for Qualitative and Multi-Method Research at the Maxwell School of Syracuse University. In 2012, CQRM will launch the Qualitative Data Repository, an NSF funded archive for qualitative social science data.
The Digital Archaeological Record (tDAR)
Digital Antiquity is a non-profit organization devoted to enhancing preservation of and access to irreplaceable archaeological knowledge. Digital Antiquity supports research, cultural resource management, education, and public outreach through tDAR (the Digital Archaeological Record -http://www.tdar.org), a digital repository for discovering, managing, preserving, and using archaeological information.
Dryad Digital Repository
Dryad is an international repository of data underlying published literature in the basic and applied biosciences.
ESIP Commons
ESIP Commons is a knowledge repository that provides publication and citation mechanisms for content generated through ESIP activities that cannot be published elsewhere. The ESIP Commons contains things like technical reports, use cases, education modules and meeting proceedings.
Fred Hutchinson Cancer Research Center
The Arnold Library provides information services and resources in support of the Fred Hutchinson Cancer Research Center's research, scholarship, educational and patient care activities.
LabArchives is an innovative web-based Electronic Laboratory Notebook (ELN) that also can serve as a repository for sharing of data sets. Under control of the user, and in partnership with EZID from the California Digital Library, LabArchives provides for the assignment of Digital Object Identifiers (DOIs) to sets of data that are stored in LabArchives notebooks. LabArchives also stores all versions of data, making it possible for readers to review older as well as more recent iterations of information.
The Long Term Ecological Research (LTER) Network Office
The LTER Network is funded by the National Science Foundation to promote understanding of environmental change via the collaborative research of over 1800 scientists and students at 26 different sites. The LTER Network Office facilitates communication and research planning across the Network and provides access to LTER data products through the Network Information System.
National Center for Atmospheric Research (NCAR)
The National Center for Atmospheric Research (NCAR) is a federally funded research and development center devoted to service, research and education in the atmospheric and related sciences. NCAR is assigning DOIs to data in order to track the use of data sets over time, give scientists and data centers credit for their work in collecting and managing data, and enable data to be discovered, accessed, and used more easily.
NASA Earth Observing System Data and Information System (EOSDIS)
The EOSIS is a key core capability in NASA's Earth Science Data Systems Program. It provides end-to-end capabilities for managing NASA's Earth science data from various sources - satellites, aircraft, field measurements, and various other programs.
PeerJ Inc.
PeerJ is an Open Access publisher of scholarly academic content. They have a journal (PeerJ) and a pre-print server (PeerJ PrePrints). Their tag line is: "Your Peers, Your Science. Academic Publishing Is Evolving" and they are committed to improving the process of scholarly publishing.
Rolling Deck to Repository (R2R) Program
The Rolling Deck to Repository (R2R) program is developing infrastructure to ensure the underway sensor data from NSF-supported oceanographic research vessels are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community.
University College Dublin Library
University College Dublin Library licenses the EZID service on behalf of the researchers and repositories hosted by University College Dublin. UCD is Ireland's largest and most diverse university with over 24,000 students, drawn from more than 100 countries. Sponsored accounts:
UCD Digital Library a repository of heterogeneous cultural heritage resources and data supporting UCD Library, UCD Archives, the National Folklore Collection, and the UCD research and cultural heritage management communities at large.
Irish Social Science Data Archive (ISSDA) ISSDA is Ireland's national centre for quantitative data acquisition, preservation, and dissemination. Based at UCD Library, its mission is to ensure wide access to quantitative datasets in the social sciences, and to advance the promotion of international comparative studies of the Irish economy and Irish society.
USGS Core Science Clearinghouse
The USGS and its collaborators Oak Ridge National Lab are providing access and management of earth science data and information to meet research and land manager needs related to ecosystems, habitats, species, climate change, and other grand science challenges.