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For Radiance, it is typical to cite the publication:
Ward Larson, G. & Shakespeare, R., 1998. Rendering with Radiance: The Art and Science of Lighting Visualization. San Francisco: Morgan Kaufmann Publishers, Inc.
For EnergyPlus, Linda Lawrie suggested this reference:
EnergyPlus Development Team. 2010. Input Output Reference: The Encyclopedic Reference to EnergyPlus Input and Output. EnergyPlus Version 6.0.
Although I have generally used this format, and obviously the year and version number would change to be the current version:
EnergyPlus Development Team, 2010. EnergyPlus engineering reference: The reference to EnergyPlus calculations. EnergyPlus Version 6.0. US Department of Energy.