Earth's Climate System: Atmosphere, Energy Balance, and Greenhouse Effect
These links address the basic physical processes of Earth's atmosphere.
Earth's Greenhouse Effect: (RealClimate; slightly technical but thorough)
Structure of Earth's Atmosphere: Similar stuff at many other sites, and in textbooks.
Earth's Energy Balance (Encyclopedia of Earth): Somewhat technical, but excellent.
Global Climate Animations (Univ of Oregon): Global Energy Balance, and other cool stuff.
NASA fact sheet on Clouds and Radiation
CO2 and radiative forcings (RealClimate; slightly technical but nicely done)
Greenhouse effect (UCAR)
Greenhouse effect (UCSD's EarthGuide)