Noam Chomsky originated Deep Structure, which plays a significant part in Neal Stephenson's Snow Crash. See The Language Instinct for more on what Chomsky meant - Deep Structure is important for reasons far more significant than its appearance in a Neal Stephenson novel!
Deep Structure was a component of early Transformational Grammar theory. Its role was gradually reduced in subsequent revisions of Chomsky's theory until finally being phased out in the nineties. Theoretical syntacticians who work outside of Chomsky's theory have never accepted Deep Structure. Presently, Deep Structure is important only as an interesting fact about the development of modern linguistic theory - which is probably less significant than its appearance in a Neal Stephenson novel. -- Steve Conley
Let's explain it a bit by an example. Let's say that "John loves Mary" and "Mary is loved by John" are synonymous. Their surface syntactic structures are different, however their deep structures are the same. Languages are much more similar at their deep structures than they are at their surface structures.
Really? Where is the evidence for the existence of these deep structures? Where is the evidence Basque and Japanese share deep structure? I don't mean handwaving, I want precisely the evidence Chomsky has so far failed to provide.
Deep Structure is also an expression used by Alan Carter in the Programmers Stone and Reciprocality Theory, in a way that is perhaps related but not directly equivalent to Chomsky's usage. It's difficult to precisely define; to get a handle on it, read the Programmers Stone, The Third Age, or this message: www.livejournal.com 
. this page said it has been deleted and purged.
-- Steve Dodd
See original on c2.com