There are many Python applications that make use of the Prototype pattern [j.mp/pythonprot], but it is almost never referred to as Prototype since cloning objects is a built-in feature of the language.
One application that uses Prototype is the Visualization Toolkit (VTK) [j.mp/pyvto]. VTK is an open source cross-platform system for 3D computer graphics, image processing, and visualization. VTK uses Prototype for creating clones of geometrical elements such as points, lines, hexahedrons, and so forth [j.mp/vtkcell].
Another project that uses Prototype is music21. According to the project's page, "music21 is a set of tools for helping scholars and other active listeners answer questions about music quickly and simply" [j.mp/pmusic21]. The music21 toolkit uses Prototype for copying musical notes and scores [j.mp/py21code].