Molecules are small pieces of structure that repeat themselves again and again. The idea has been around for a long time, but was formalized by Jim Hines in the 1990s. Basically Jim posed the question "why are experienced modelers so much faster at developing models than beginners?" The answer he came up with was that experienced modelers have building block structures stored in their heads that make it much easier to formulate most equations. He called these elements of structure Molecules.
The molecules themselves are not part of Vensim. What Vensim provides is a mechanism to open and review the molecules. You can also, if you wish, extend or even replace the molecules with your own.