The best reference I found on quotations was the quotation section in Larry Trask’s Guide to Punctuation. Alongside clarifications [ ] and suspensions … it contains rules on fun things like quotes in quotes, when to capitalise, dealing with mistakes [sic], adding emphasis [emphasis added], and punctuation inside or outside. On this last point he suggests:
You may follow your own preference in this matter, so long as you are consistent. If you opt for logical punctuation [putting the punctuation outside the quote], you will have the satisfaction of knowing that you are on the side of the angels, but you should also expect some grim opposition from the other side [that prefers punctuation on the inside].