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"make a monkey of someone", " don't monkey with that lock!", and "where have you been, you little monkey!" are examples of sentences where monkey have different meaning.

Should the comma be placed inside the quotes, or outside?

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American style is to place the comma inside the quotes. This is universally the case in publishing and accords with all style guides (Chicago, AP, NYT, etc.). The only exception is is in academic works, particularly philosophy texts, where a word is being specially defined and offset with single quotes. That exception, however, is not widespread and some houses, such as Oxford University Press, use the single quote as closing punctuation.

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The punctuation-inside rule has always irritated me to no end, even before I got into programming. This is one of many illogical, yet "proper" rules that exacerbate confusion of the English language. –  David Rivers Mar 3 '11 at 6:40
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American usage is "yes," it should be inside the quotes even if it is not part of the quotation. British usage has it outside unless it is part of the quotation (as far as I know).

Note that it is becoming increasingly common in American usage to move the comma outside of the quote because there is a growing subset of the population who use string literals in programming and the comma is not part of the data. The "Comma in the Quotes" rule is still expected however.

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I personally always use punctuation-outside-of-quotes format (unless the punctuation was part of the original text) for exactly the reason you specify: as both a writer and a software guy, I find it misleading and imprecise to include punctuation inside quotation marks that isn't actually part of the quote. –  Uncle Mikey Mar 1 '11 at 22:51
    
I usually use out-of-quotes for phrases. For an extreme version of punctuation within quotes, see this 1915 statistics paper which mentions a pseudonym-using writer called "Student" with quotation marks as part of his nom de plume. Examples in the text include "Student's", "Student,", "Student." and even "Student†". –  Henry Mar 1 '11 at 23:30
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