Unfortunately, the "surface" appeal of the Deep Structure concept soon led people from unrelated fields (architecture, music, politics) to misuse and abuse the term to express various things in their own work, which rarely if ever had the rigor of Chomsky's own linguistic scholarship. Perhaps it was this situation that led Chomsky and his students to abandon the term entirely, replacing it with the abbreviation "DS".
In 1980 and 1981, Chomsky's theory took a new turn, becoming known as Government and Binding Theory (the name is somewhat misleading, since Government and Binding are not the only significant components of the theory). In his book Barriers, Chomsky attempted to unify various (technical) concepts in GB theory which had previously been separate. In 1993 he published an extremely significant paper, The Minimalist Program, (not to be confused with the 1995 book of the same name) which proposed the use of economy conditions in syntax to a greater extent than had previously been considered.
Current Chomskyan linguistics focuses on relating various representations (meaning, structure, sound) to each other in a way that doesn't make any of them deep or fundamental. Hence, one way to make yourself look pretentious, misinformed, and tragically unhip to a group of linguists is to say something about the "Deep Structure" of the mind, supposedly revealed by Chomsky. To be fair, this is more a matter of nomenclature than anything else, as the most robust (and controversial) notion put forth by Chomsky has been the concept of a "Universal Grammar" that constrains the overall forms of linguistic expression available to the human species. This concept -- more of a grammar-schema than a grammar -- is probably what non-linguists are referring to when they say "Deep Structure". This usage seems quite natural and appropriate, but it is rather liable to cause unnecessary confusion.
It is in early works such as these that the original concept of the deep structure/surface structure distinction is presented. For an account of more current ideas in transformational grammar, see