A Polygon soup is a group of unorganized triangles, with generally no relationship whatsoever. Polygon soups are the default output format when geometry is exported from a 3D modeling package, such as Maya or Blender

Blender (software)

Blender is a free and open-source 3D computer graphics software product used for creating animated films, visual effects, interactive 3D applications or video games. The current release version is 2.60, and was released on October 19, 2011...

. As soon as any kind of hierarchical sorting or clustering scheme is applied, then it becomes something else (one example being an octree

Octree

An octree is a tree data structure in which each internal node has exactly eight children. Octrees are most often used to partition a three dimensional space by recursively subdividing it into eight octants. Octrees are the three-dimensional analog of quadtrees. The name is formed from oct + tree,...

, a subdivided cube). Any kind of polygonal geometry that hasn't been grouped in any way can be considered polygon soup. Optimized meshes may contain grouped items to make drawing faster.