YARGH. Okay so this is one of the primary areas of research that one of my professors from university studies (
http://www.ling.ohio-state.edu/~croberts/ ).
None of the explanations that people have written here are entirely correct or reflect what's actually going on.
The phenomenon that's being discussed here is something called Contrastive Stress. It is a part of an interesting area of research on Linguistic Focus (http://en.wikipedia.org/wiki/Focus_(linguistics)) that sits at the juncture of Semantics (meaning in abstract), Pragmatics (meaning in context), and Autosemgental Phonology (mental representation of sounds and their production of non-phoneme related stuff).
So, contrastive stress ties directly into the notion that sentences are stated in response to either explicit or implicit questions. In fact the location of the emphatic stress is directly related to what question the speaker is trying to answer.
So, you can actually do this with nearly any sentence, simply by placing the stress on a different word.
Badger's account is mostly correct, but it's tied in a little closer with grammar than his examples actually intimate. I'd say that there's a much wider range of possible candidates for say:
Did you say she stole your money?
I didn't say she stole my money, i know/saw/heard/thought/wrote/hinted/testified/dreamed it!
"It" in this context is the entire grammatical structure "she stole my money". The reason why this is important is because of the notion of what can be stressed and what the stress is actually applied/scoped to.
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You can do this with other sentences as well:
George W. Bush is the 43rd President of the United States.
"Is jeb bush the 43rd president of the united states?"
No, George Bush is the 43rd President of the United States.
"Is George Washington the 43rd President of the United States?"
No, George Bush is the 43rd President of the United States.
"George Bush isn't the 43rd President of the United States, right?"
No, George W. Bush is the 43rd President of the United States.
"Was there more than one 43rd president of the united states?"
No, George W. Bush is the 43rd President of the United States.
"Was George W. Bush the 44th President of the United States?"
No, George W. Bush is the 43rd President of the United States.
"Was George W. Bush the 43rd Vice President of the United States?"
No, George W. Bush is the 43rd President of the United States.
(okay, so "of" is a function word that we can't contrast against anything else)
"Was George W. Bush the 43rd President of the United Arab Emerates?"
No George W. Bush is the 43rd President of the United States.
etc.
So this really is a general phenomenon that you not only see every day, but really use on a constant basis. Every sentence has grammatical stress, it's how we know what other people are focusing on when they speak.