Physics
HEP Data - high-energy physics reaction database of Numerical HEP scattering cross sections
NIST Physical Standards Laboratory - physical reference data and property tables
National Nuclear Data Center - includes nuclear structure, reaction and decay databases
Astronomy
HEASARC - NASA's High Energy Astrophysics Science Archive Research Center
Infrared Science Archive - NASA's science and data center for infrared astronomy
Extragalactic Database - NASA's archive of data for over 3 million extragalactic objects
Virtual Astronomical Observatory - Astronomical data from ground and space-based telescopes. Includes data analysis tools
National Space Science Data Center - Archive for NASA space mission data
Sloan Digital Sky Survey - Download optical images of the sky. See also, SkyServer for educational portal to the data.
Engineering Strong Motion Data Center (CESMD)
Space Science and Engineering Data Center at the University of Wisconsin-Madison
The University of Florida Sparse Matrix Collection
Clean Energy Project Database "The Clean Energy Project Database (CEPDB) is a massive reference database for organic semiconductors with a particular emphasis on photovoltaic applications." (taken from databib.org)
The Cooperative Association for Internet Data Analysis "CAIDA" curates datasets resulting from both active and passive measurement of the Internet." (From their website)
DOE datacenters OSTI is the DOE official data-center for storing DOE funded research.
MatDB - A European Union based materials database.