These are open source software projects of ours or academic publications that include their source code.

Pepr3D is an intuitive, free, and open-source 3D painting tool for coloring models intended for colorful 3D printing
SmallUPBP is a small physically based renderer that implements the unified points, beams and paths algorithm described in the paper "Unifying points, beams, and paths in volumetric light transport simulation".
Morphome3cs II is a software project developed in cooperation of CGG - Computer Graphics Group, Department of Software and Computer Science Education, Faculty of Mathematics and Physics, Charles University in Prague and 3DLAB - Laboratory of 3D Imaging and Analytical Methods, Department of Anthropology and Human Genetics, Faculty of Science, Charles University in Prague Its aim is the integration of the functions such as landmark and curve placement, the statistical analysis of this data and presentation of results. A noteworthy part is also the tool for dense mesh analysis that works directly with surface models. Morphome3cs is an integrated environment for research in anthropology and archaeology as well as a solid testbed for new registration and visualisation methods.
SmallVCM is a small physically based renderer that implements the vertex connection and merging algorithm described in the paper "Light Transport Simulation with Vertex Connection and Merging"
Source code implementing the sky dome luminance model described in the 2012 paper "An Analytic Model for Full Spectral Sky-Dome Radiance"
Stubble is a plugin for Autodesk Maya providing user-friendly virtual hairstyling, i.e., creation, editing, and animation of hair or fur on 3D models
Radiance Caching is a ray tracing-based method for accelerated global illumination computation in scenes with low-frequency glossy BRDFs. The method is based on sparse sampling, caching, and interpolating radiance on glossy surfaces. In particular we extend the irradiance caching scheme proposed by Ward et al. in 1988 to cache and interpolate directional incoming radiance instead of irradiance. The incoming radiance at a point is represented by a vector of coefficients with respect to a spherical or hemispherical basis
GrCis is repository of computer graphics algoritms and exercises in C# language maintained by by Josef Pelikán. It is used in computer graphics labs (see CG I, CG II, ..) taught by Josef Pelikán