So let’s say I’m writing an essay involving The Jungle, although the subject is only tangentially related to my question. If I have a sentence constructed similar to:
Should that comma after “hoboing it” be placed inside or outside the quote marks? (Upon preview, it has occured to me that the comma is probably unnecessary altogether. For the sake of argument, pretend that it’s not, please, since I can’t think of a better example right now.)
Inside, and it’s not unnecessary. A comma and a conjunction are the minimum you need to separate two clauses.
By the way, that first clause is in the passive voice, something careful writers avoid. 
The comma goes inside the quotation marks in American usage, outside them in British usage. (On whether the comma is necessary at all, you can find authorities on both sides.)
I’ll cross the proofreading bridge when I come to it. 
Thanks to both of you!
I disagree as to whether the comma is needed. In my opinion, it is. Without ithat comma, the reader would be compelled (briefly)to sort out (what seems to be) the two objects of the verb “hoboing”: “it” and “Jurgis.” With the comma, that ambiguity is made clear. I think it belongs.
“ithat” = “that”
The red salamander has it – use commas when even momentary ambiguity would otherwise result.
As for the “passive voice” nitpick, the stylistic guideline is against unnecessary use of the passive voice.
The focus of the sentence is on what Jones was presumed to be doing, not on who was doing the presuming. It may not be the wisest sentence in the world, since it immediately raises the question, absent context, of who was in fact doing the presuming. But as it stands, it’s a proper use of the passive. The key point is what the focus of the sentence is, and how the verb relates to that focus.
From The Blue Book of Grammar and Punctuation, www.grammarbook.com:
I agree with pseudotriton and Polycarp that the OP’s sentence reads clearer with a comma than without. But if it were written without a comma, it may not read as well, but it would not be grammatically incorrect.
Unfortunately, some American universities (coughYalecough) teach punctuation the British way which causes a lot of confusion. I work for attorneys, and as if it isn’t difficult enough to read their handwriting, I have to figure out where they went to school in order to punctuate for them “correctly.” There’s nothing worse than to have to go re-punctuate an entire document for no better reason than the attorney graduated from Yale.
If you are writing something for yourself, just be consistent. If you are transcribing for someone else (especially an attorney), find out their preference.
I would use quotes. It is absolutely idiotic to punctuate inside quotes unless the punctuation belongs to the thing quoted (not relevant here) and I refuse to do it. Yes, that is the standard, but if the standard is senseless (and in the case of a direct quote wrong besides), then the only way to change it is to stop doing it. Otherwise it just goes on and on and on. Just because everyone has always done it wrong is no reason to continue doing it wrong.
Hari Seldon
If it’s any consolation, the issue is still debated regarding UK English. Generally, the UK convention is to use inside for direct quotes, and outside for indirect quotes …
a) She said, “You must quote me correctly.”
b) She said that I must quote her “correctly”.
… but there’s a long-standing alternative view (which I agree with, but don’t always have the nerve to use) in favour of nesting quotes logically, as you describe:
c) She said, “You must quote me correctly”.