I thought readers might like to see how different style guides address the general question of how to position footnote callouts (termed "cues" in The Oxford Guide to Style, "note numbers" in The Chicago Manual of Style, and "references" in Words into Type). Here is a quick rundown of the relevant passages from one British and five U.S. style guides.
From The Oxford Guide to Style (2002):
Note references can be cued in several ways. The most common is by superscript figures or letters. Place in-text cues outside punctuation, but inside the closing parenthesis when referring solely to matter within the parentheses. Normally cues fall at the end of a sentence unless referring only to part of the sentence: a cue at the end of a sentence represents the whole of a sentence:
Causes for infection were initially thought to be isolated.16 (This as rapidly discredited.17) Even so, specialists in England18 and Wales19 reached different conclusions during subsequent tests.
From The Chicago Manual of Style, sixteenth edition (2010):
14.21 Placement of note number. A note number should generally be placed at the end of a sentence or at the end of a clause. The number normally follows a quotation (whether it is run in to the text or set as an extract). Relative to other punctuation, the number follows any punctuation except for the dash, which it precedes.
"This," wrote George Templeton Strong, "is what our tailors can do."1
The bias was apparent in the Shotwell series3—and it must be remembered that Shotwell was a student of Robinson's.
Though a note number normally follows a closing parenthesis, it may on rare occasions be more appropriate to place the number inside the closing parenthesis—if, for example, the note applies to a specific term within the parentheses.
(In an earlier book he had said quite the opposite.)2
Men and their unions, as they entered industrial work, negotiated two things: young women would be laid off once they married (the commonly acknowledged "marriage bar"1), and men would be paid a "family wage."
[[The logical superiority of the Oxford system to the Chicago system should be evident from this incidental use of footnotes in Chicago:
14.4 Electronic resource identifiers. When citing electronic sources consulted online, Chicago recommends—as the final element in a citation that include all the components described throughout this chapter and in chapter 15—the addition of a URL1 or DOI.2
For more information about URLs, consult the website of...
For more information about DOIs, consult the websites of...
In this instance, Chicago clearly means for its footnote 2 to apply only to the word "DOI" in the sentence where the callout for footnote 2 appears. That being the case, Oxford would have advised putting the superscript 2 inside the end punctuation; but Chicago's less precise rule requires putting that number outside any end punctuation. Consequently, Chicago's method is incapable of distinguishing between a footnote that refers to the final portion of a sentence and a footnote that applies to the entire sentence.]]
From [Merriam-]Webster's Standard American Style Manual (1985):
Placement of the Elements
Footnotes and endnotes to a text are indicated by unpunctuated Arabic superior numbers (or reference symbols, discussed later in this section) placed immediately after the quotation or information with no intervening space. The number is usually placed at the end of a sentence or clause, or at some other natural break in the sentence when the material is not a quotation. The number follows all marks of punctuation except the dash. If a terminal quotation mark appears (as at the end of a short quotation that is included in the running text), the numeral is placed outside the final quotation mark with no space intervening [cross reference omitted].
From Words into Type, third edition (1974):
Position of references. Reference figures or marks should be set after any mark of punctuation except the dash or a closing parenthesis if the reference relates to matter within the parentheses. They should be placed after, not before, a word or paragraph that is explained or amplified.
Reference to the footnote citing the source of an excerpt should stand at the end of the excerpt, not in the text that precedes it. Thus placed, the reference does not distract the attention of the reader as it would elsewhere.
From Hodges' Harbrace Handbook, revised thirteenth edition (1998):
Both footnotes and endnotes require that a superscript number be placed wherever documentation is necessary. The number should be as near as possible to whatever it refers to, following the punctuation (such as quotation marks, a comma, or a period) that appears at the end of the direct or indirect quotation.
From MLA Style Manual and Guide to Scholarly Publishing, second edition (1998):
A.2 Note Numbers
... Format note numbers as as superior, or superscript, arabic numerals (i.e., raised slightly above the line, like this1, without periods, parentheses, or slashes. The numbers follow punctuation marks, except dashes. In general, to avoid interrupting the continuity of the text, place a note number, like a parenthetical reference, at the end of the sentence, clause, or phrase containing the material quoted or referred to.
The style guides I consulted are effectively unanimous in agreeing that, when a footnote comprehends the entire sentence or clause at whose end the footnote callout is to appear, the callout superscript number or mark should appear after any punctuation marks that appear at that point—unless the punctuation mark in question is a dash or (in some guidelines) a close-parenthesis mark.
The style guides disagree about where to place the callout number or mark when it comprehends only part of the sentence or phrase where it appears, with Oxford offering the most logical and granular approach to dealing with such situations and most U.S. style guides recommending a less precise treatment.
Publishers' house styles vary considerably on the question of handling callouts that apply to only part of a sentence. The publisher I currently work for takes what may be the most extreme approach I've seen: when a manuscript includes sentences with internal footnote callouts that apply to only part of the sentence in which they appear, the publisher insists on either moving the footnote to the end of the whole sentence (outside the end punctuation)—and in instances where the author had marked more than one internal callout to occur in a single sentence, consolidating the footnotes into a single, longer footnote—or breaking the original sentence into two or more shorter sentence and assigning the footnote callout to the appropriate shorter sentence (again, outside the end punctuation). Because the publisher is not a scholarly press and because it deals with institutional rather than individual academic authors, it can dictate this sort of intervention without prompting an author rebellion, but I don't recommend this approach for most situations.