Three of them are The Chicago Manual of Style, and a more badly organized, awkward to use, and inconsistent between editions reference manual it would be hard to find. The other two are the MLA Style Manual, and that's easier to use but vastly misunderstood.
About fifteen years ago I had a scholarly paper published which included a lot of quotations, and many of those quotations were heavily abridged. As a result, it had a lot of ellipses in it. The editor of the journal surrounded all those ellipses with brackets, so that they looked like this: "Three rings for the Elven kings under the sky [...] One for the Dark Lord on his dark throne."
This practice was, then, entirely new to me, and I thought it was the ugliest thing I'd ever seen. Obviously it was to distinguish my supplied ellipses from any that happened to be in the original (not that the editor asked me if any were), but since original ellipses are rare, this seemed to me a bass-ackwards way of making the distinction; if an ellipsis is in the original, that could be noted in the citation.
Subsequently I started seeing it more and more, and I've been told, even quite recently, that this is MLA style. It wasn't MLA style when I learned it years ago, but apparently it was added, and anybody following MLA style, well, that's what they gotta do, like it or not.
But here's the thing. It isn't MLA style. Not any more, and not for several years now. It is indeed in the 2nd edition of the manual (1998), which came out just before my paper was mutilated. But they took it out of the 3rd edition (2008). Perhaps there had been complaints. Now all it says is that "some publishers prefer" the brackets on supplied ellipses, and it's an option to distinguish supplied ellipses from original ones in the rare case where a quotation contains both; the other option, surprise surprise, is to note in the citation the presence of original ellipses.
There are other things in MLA3 that aren't in MLA2 that I've never seen applied in scholarly papers either, so I have to conclude that nobody's ever read MLA3.
Another weird thing I've occasionally come across is bitter complaints by humanities scholars against the author-date citation system, whereby books you cite are identified in text references by the author's name and the year of publication. This kind of makes sense in science, where the age of the source material is often crucial, but it's particularly insane when dealing with a posthumously prolific author like Tolkien. It's unfortunate, to say the least, for a paper to distinguish between, say, The Book of Lost Tales, which was written during WW1, from the Grey Annals of Beleriand, which were written in the 1950s, by citing them as "Tolkien 1983" and "Tolkien 1994" respectively, because that's when the books they're in happened to be published. But I've seen journals that insist on exactly that.
What's weird is that the people who complain about this say it's MLA style. But it isn't. It's Chicago science style, which Chicago used to (14th ed., 1993) claim was growing in popularity in the humanities as well, but more recent editions (15th, 2003; 16th, 2010) have given up on that, offering as an alternative the antiquated footnotes style ("17. Ibid.") that MLA gave up on back in the 1970s, I think. MLA uses a shortened author/keyword inline style, thus:
Bilbo tells the dwarves their entire adventure is "silly" (Tolkien, Hobbit 247)and if you want to know the full title and which edition is being cited, consult the bibliography. That's MLA style, and it makes sense. (And if you're citing just one work by an author, you don't even need the keyword.)
A little more of this sanity to go around the table, please.