oh this is a good question... weirdly enough, i was not super huge into webcomics in my middle school years. there are two specific "internet pieces" i will mention that i sometimes still think about to this day:
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there was this twilight princess series on fanfiction.net that had the most insane prose i have ever read on that website. the author titled it "the moments trilogy" which i think started as an innocent sort of oneshot, but then it evolved into this gritty postgame AU where midna never changes back into her normal form and she and link and the population of kakariko village have to wage war against king bulbin's forces and then zelda decides to turn against the common hylian and i cannot even BEGIN to describe how crazy it gets, but it is a wild ride from beginning to end. it was peak 2007 energy and i say this in the best way possible. i occasionally come back to it from time to time and am surprised at how well the prose has held up (ymmv on the story). that author was IN COLLEGE when they wrote that series and i do hope they ended up writing novels of their own because i imagine their writing skills got exponentially better from there.
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this probably isn't quite what you're looking for but. there was this short persona 4 souji x yosuke comic on tumblr that i used to re-read... it is probably lost to the sands of time at this point, but it was basically the concept of yosuke going back in time whenever he screwed up the p4 timeline and after some number of loops he just loses it on the first day of meeting souji and says something along the lines of "i've loved you a hundred times in a hundred worlds but i have no idea how to get it right" and the style and the expressions were just so well done. thinking about it still gives me a good kick in the feelings, which is pretty impressive because that game aged like milk to me.