Strunk and White's
Elements of Style is usually regarded as the definitive reference for copy editors.
http://orwell.ru/library/others/style/index.htm
This online version is more devoted to the actual writing style than grammatical rules, but worth a read for any writer.
This excerpt covers mainly comma rules for parentheses and quotes:
Quote:
Parentheses. A sentence containing an expression in parentheses is punctuated outside the last mark of parenthesis exactly as if the parenthetical expression were absent. The expression within the marks is punctuated as if it stood by itself, except that the final stop is omitted unless it is a question mark or an exclamation point.
I went to her house yesterday (my third attempt to see her), but she had left town.
He declares (and why should we doubt his good faith?) that he is now certain of success.
(When a wholly detached expression or sentence is parenthesized, the final stop comes before the last mark of parenthesis.)
Quotations. Formal quotations cited as documentary evidence are introduced by a colon and enclosed in quotation marks.
The United States Coast Pilot has this to say of the place: "Bracy Cove, 0.5 mile eastward of Bear Island, is exposed to southeast winds, has a rocky and uneven bottom, and is unfit for anchorage."
A quotation grammatically in apposition or the direct object of a verb is preceded by a comma and enclosed in quotation marks.
I am reminded of the advice of my neighbor, "Never worry about your heart till it stops beating."
Mark Twain says, "A classic is something that everybody wants to have read and nobody wants to read."
When a quotation is followed by an attributive phrase, the comma is enclosed within the quotation marks.
"I can't attend," she said.
Typographical usage dictates that the comma be inside the marks, though logically it often seems not to belong there.
"The Fish," "Poetry," and "The Monkeys" are in Marianne Moore's Selected Poems.
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-Mikey