There is a reason this is called a punctuation guide. It attempts to provide guidance, rather than black-and-white rules. The grammatical use of punctuation is fairly settled; punctuation style, on the other hand, is variable.
In the United States, the leading style guides are The Chicago Manual of Style and The Associated Press Stylebook. The former is widely adopted throughout the publishing industry; the latter is mostly used by news organizations. Both are available in print and online, though not for free. Some scholarly and professional organizations have their own style guides, though these usually focus more on documenting references than on punctuation. Writers short of cash, as well as those preparing documents for the United States government, should consult the United States Government Printing Office Style Manual, which is available for free at http://www.gpo.gov/fdsys/pkg/GPO-STYLEMANUAL-2008/content-detail.html.
When style issues are implicated in this guide, I have usually deferred to The Chicago Manual of Style, 16th edition. The few deviations are noted within the guide.
The following chart shows some of the major differences in punctuation style between The Associated Press Stylebook (2011 edition) and The Chicago Manual of Style (16th edition).
The Chicago Manual of StyleThe Associated Press StylebookInclude a comma before the conjunction. My favorite composers are Beethoven, Brahms, Mahler, and Mozart.Do not include a comma before the conjunction. My favorite composers are Beethoven, Brahms, Mahler and Mozart.Serial commaDo not include a space between initials. E.L. DoctorowSpacing between initials in namePreference for periods. J.D., B.A., Ph.D., B.C.E., P.O. Box, U.S., U.N. AbbreviationsInclude a space between initials. E. L. DoctorowPreference against periods. JD, BA, PhD, BCE (referring to the era), PO Box, US, UNAdd an apostrophe and s unless the next word begins with s. Actress’ scenePossessives of singular nouns ending in sAlways add an apostrophe and s. Actress’s scene Add only an apostrophe. Texas’, James’, Xerxes’Possessives of singular proper nouns ending in sAdd an apostrophe and s. Texas’s, James’s, Xerxes’s