girl genius is a pretty tiny fandom and if you’ve found persephone_kore and khilari on AO3 you have found the major good-fic producers. there are good shorter or single fics in the AO3 section by other authors, but that’s pretty much all there is. the kink meme’s fics mostly get reposted on AO3 too and i don’t remember having seen anything unique to the kink memes.
tumblr-only there’s setaripendragon who has two especially fun stories, one where Klaus and Gil meet Zeetha at the circus (ahh family feels) and an AU where the trio are away at college and their parents come for christmas – which includes Klaus, Zantabraxus, Adam and Lilith, and Majorly Narcissistic Mom Lucrezia – as they try to hide their ot3 lovin’ ways. (i don’t remember if they wrote other fics too but it’s worth going to explore cause good writing. plus they have sipderman/deadpool fic if you’re into that.)
as for homestuck i guess explore my pimptastic tag or look through my AO3 bookmarks? nothing comes to mind that everyone else hasn’t read already and there’s like four years of fandom history there and my bookmarks are pretty much “when i remember the feature exists” so they’re not an exhaustive list either, but if i pimp or bookmark it, i liked it.