I have found that, without question, the most popular post on this blog was about using footnotes on the iPad. However, that post is very old, and some new things have happened since then.
I will assume that it is primarily academics and a handful of other professionals who need to know how to use footnotes on the iPad, so I will tailor this discussion to them. In short, the best app for footnotes on the iPad is still Pages. All you have to do is point where you want the note, press the “+” button on the lower right of the screen, and select footnote. It is as easy as it gets.
That is not to say that there are not some real problems with Pages, and I would say that using Pages is only practical if you also have Pages on your computer, which means that you need a mac. I say this because the Pages defaults are wildly stupid, and many cannot be changed on your iPad. For example, the main problem with the footnotes is that Pages automatically puts an extra line break in between your footnotes. I suppose that this is not the worst thing, and you can transfer the document to a Word format and it will be fine; it just drives me crazy. Why is that the default?! Why can’t I change it on my iPad?! The only way to avoid the problem is to create a document formatted the way that you want it on your home computer and send it to your iPad. In fact, that is the only way in which writing on your iPad is ever going to be practical. Format some documents the way that you want them on your computer, and then use them like templates on your iPad.
The main reason that I say that you need Pages on your computer is because you do not want to be translating Pages to Word, back and forth, to work on your iPad and on your home computer. It adds in a variety of problems with formatting and styles. When I write, I do it all in Pages and transfer it once to Word. That seems to work well.
There are some other options for footnotes on the iPad, but they are less practical. Quickoffice does not have them at all, so forget that. Docs2Go will display your footnotes and it will let you add them, but there is no way to edit them. Once they are in there, there is no changing them. Also, it changes my font when I move a Word document to Docs2Go. Next!
HopTo seemed promising, but it does not appear to have any footnote functions. GoDocs, which allows you use your Google docs, will allow you to use footnotes, but it is buggy (when I changed my gmail password after the heartbleed fiasco, I had to delete the app and reload it because it got stuck trying to log me in) and awkward to use. In order to insert a footnote, you need to use the desktop version (as opposed to mobile) of the document editor, which does not work well with the iPad pop-up keyboard. It is better if you have a bluetooth keyboard. This is a workable option, but not as clean or easy-to-use as Pages. Also, what if I need to work away from a wifi connection? I am not sure how well it would work.
Finally, you do now have the option of using the entire Microsoft Office suite on your iPad. I have not used it, but it claims to have the full usability of the desktop software. Reviews on the iTunes store are mixed, but I imagine that it does the job. The problem, for me, is the price. There is a minimum subscription of $7/month. That would be $84/year, every year. The iWork suite is free (or $10 per app, depending on when you bought your computer) for the desktop computer and $10 per app for the iPhone or iPad (with three apps, that is $30) to buy them forever, and they work on as many devices as I want. With the Microsoft $7 subscription, the Office suite works on only one mobile device.
I have done my share of cursing at Pages and Numbers (I generally like Keynote). The newest versions are less intuitive and powerful than the older versions. They have idiotic defaults. Apple clearly cares more about making them pretty than functional. The apps are not backward compatible and every few years I have to open and resave relevant Pages documents so that they can be usable on my iPad and the current version of Pages on my computer (this one really makes me angry; if I can open a paper I wrote in high school using Word, why can’t I open something I wrote two years ago on Pages?!). However, the iWork suite in general and Pages in particular are the most practical solution for academic and professional work on the iPad. If you must use Office and price is not a problem, buy a Microsoft subscription. If you think that Microsoft already gets too much of your money, go with Apple. That may be the first time anyone has ever said that.