The title is the question. Somehow I should know the answer, but I am by no means sure what is meant exactly by it. Perhaps it doesn't have a definite meaning and only in context, could someone provide examples? For instance is the following use of the term acceptable: the structure maps of a direct limit/fibred product/whatever are the morphisms that form part of the direct limit/fibred product/whatever, i.e. which are "part of the structure of the direct limit" (I mean by definition a direct limit is an ordered pair consisting of an object and a family of morphisms having some properties). See also https://mathoverflow.net/questions/42241/errata-for-atiyah-macdonald, the answer by Georges Elencwajg.
I am aware of only one "official use" (abuse of the word): in EGA when defining the category of $S$-objects: the $S$-objects are morphisms $X\rightarrow S$ and informally one refers to $X$ as a $S$-object and the morphism $X\rightarrow S$ as "the structure map of $X$".
A structure map is a map which is being specified as part of a structure!
For example, as you say, a scheme over a scheme $S$ is a scheme $X$ equipped with a map $X \to S$; that map specifies the structure of being a scheme over $S$ and so is the structure map. Similarly, a limit or colimit is an object equipped with maps such that etc., and those maps specify the structure of being a limit or colimit and so are the structure maps.