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This blog post should be a good primer on footnotes  
However, my adblocker seems to have gone nuts and the footnotes aren’t rendering properly—I think it is allergic to whichever CDN delivers the JS that makes the footnotes work.  
In theory, the notes and citations should be pop-ups that neither make you lose your place nor require a secondary tab open.

I’ve actually thought about this before. David Foster Wallace is one of my favorite writers and his extensive use of footnotes and endnotes have, consciously and/or unconsciously, gotten me to use them more frequently as well.
 
The simplest approach I could think of for sites like fimfiction would be to perhaps use endnotes rather than footnotes. In other words, you would put all the notes in their own “chapter.” It requires the reader to have two tabs open, one for the text proper and the other for the notes, but that’s probably easier to deal with than asking them to scroll up and down constantly or whatever inconveniences any other workaround would entail.

What is your opinion on footnotes in fanfiction? Are there fanfiction repositories that have on-click or hover popovers for footnotes and references, like the blog Wait But Why? Fimfiction uses footnotes that appear at the end of the chapter. However, unlike Wikipedia citation footnotes, they are not hyperlinked so you cannot easily flip back and forth between the footnote and resume your place in the chapter.
 
I’m struggling my way through reading House of Leaves. That book uses extensive lengthy footnotes both as an integral storytelling mechanism and as citations referencing other works, both real and fictional. My writing style without proper hoofnote support often ends up very wordy with far too many sidebars and parenthetical asides. Footnotes allow you to add all that flavor text without interrupting your prose or main storytelling. House of Leaves has me inspired to make use of the footnotes in my own works rather than avoid them by shoving everything into the main narrative.