I've searched for fan fiction in the following fandoms: Star Wars, Star Trek, Mass Effect, The 100, Bioshock, Borderlands, and Dragon Age.
I don't read Star Wars fanfic, and have not read much of the pro material. Splinter of the Mind's Eye was a decent story (also written by Alan Dean Foster), and so were the Han Solo books. To my recollection, the last Star Wars book I read was an anthology about the Mos Eisley cantina, edited by Kevin J. Anderson. He should have stuck to Star Wars, since he can't write Dune. I've tried some The 100 fanfic, and found it uninteresting. Other than Star Trek, I don't know what the rest of your list even is.
Star Trek is a category all by itself. Which series, which characters? TV or movies? Classic Trek, Berman-era, or nuTrek? I've found nuTrek crap miscategorized on fanfiction.net - there's a section for it, but some of it's been posted in the TOS section. It's very annoying when I expect to read a story about Uhura at Starfleet Academy and discover it's one of those stupid nuTrek ones where nuUhura and nuSpock are living together and having soapy sitcom nonsense going on.
But I've found some really good stuff on fanfiction.net, as well. There's a story about Tasha Yar's years at Starfleet Academy, and it explores her friendship with Worf, her PTSD (due to the ordeals she suffered on her home planet, Turkana IV), and her determination to succeed. It's a terrific story... for as long as it lasts. The author never finished it.
I don't read much DS9 fanfic, and most of the TOS fanfic I've ever been into has been the early stuff from the '70s. I have that in physical 'zine form, which is better than the online version since the original illustrations are part of it, along with the poetry, songs, comics, and miscellaneous content.
Voyager stories... yep, definitely a guilty pleasure, as long as it's not sappy Janeway/Chakotay romance. There's someone over at TrekBBS who has written a pretty good series of adventure stories that take place post-Endgame, in which the junior officers are the main characters. Harry and Tom work their way up the ranks in Starfleet and Tom Paris eventually gets his own command. There's a fair bit of crossover with TNG, and some of the stories involve Tom's ship dealing with Andorians, Orions, and other classic Trek aliens.
I'll grant that you're unlikely to find good Star Trek content at Archive Of Our Own. I haven't found anything there. The sites I use are fanfiction.net, Orion Press, the Valjiir Continuum website, and numerous others.
The nice thing about fanfiction.net is that there are so many shows, movies, and books that people write about, that you're apt to run across just about anything. I found a crazy crossover of Keeping Up Appearances/Murder, She Wrote. Somebody murders Hyacinth Bucket (pronounced "bouquet"), and Jessica Fletcher has to figure out whodunnit. Since hardly anyone on the show can tolerate Hyacinth for more than a few minutes at a time, the suspect list is pretty long.
The thing about fanfic is that unless the author is very, very good, you're not going to find professional-grade stories, or at least not the kind of stories that would have been shown on TV. All the Bonanza stuff I mentioned earlier would never have been on TV because it was a staple of the show that none of the Cartwright men were ever to get married. They could flirt, have an affair (as discreet as late 1950s/mid-1960s standards would allow), or become engaged. But marriage was out of the question. That's one reason why Pernell Robertson left the show; he was frustrated at how his character was in his mid-30s, still subordinate to his father, and never allowed to marry or set up his own household. The fanfic stories took care of that, giving the Cartwright sons their own households, wives, children, even grandchildren. Some even gave Ben a fourth wife, or a previously-unknown child turned up from some brief affair in one or another episode.
The point of fanfic is to have more of what you like about whichever show, movie, book, etc. you're into. The stories can be serious, romantic, adventurous, funny, tragic, some combination of those... a lot of the Voyager fanfic gets written because people don't like the way the show ended. They got to Earth, then... nothing. That was the end of the series, and although the novelverse picked up where the show left off, that's an unsatisfying direction as well. There's too much intrusive material from TNG in the Voyager novels. Therefore, I read Voyager fanfic that has minimal input from TNG characters.
Disclosure: I can't seem to write serious Star Trek fanfic to save my life. It always veers off into the direction of parody or satire. So fine. I'll write about Captain Jacquard and Bill Biker of the U.S.S. Surprise! (a parody series a friend and I started back in 1989 for our local club newsletter I edited). It's not even slightly serious, the humor is dumb, and it's cathartic since I get to mock all those pretentious, uptight Next Gen characters.
I've looked for these on Wattpad, Archive of Our Own, Quotev, and FanFiction. I have read a fanfic written by a friend which was decent reading but didn't really feel like a fanfic to me (the source material was at best a passing mention).
You've barely scratched the surface, in the case of Star Trek. There's a fanfiction subforum over at TrekBBS, and I've read some good stories there. The last one was about McCoy spending six months aboard an all-Vulcan science ship, to do research on the Fabrini medical knowledge he recovered from Yonada. It's one of these fish-out-of-water stories and a pretty decent character study that explores McCoy's tendency toward casual bigotry toward Vulcans.
Generally speaking I'm not interested in "[Character] but different!" or weird romances that don't make any sense. Most of what I come across fit into either or both of those categories. The latest fanfic recommended to me by someone was a short story featuring General Hux and Kylo Ren from the new Star Wars trilogy. It depicted Hux as an anxious panic-ridden wreck and Kylo as some domineering type, and as you can expect it was all about how Kylo solves Hux's panic attacks through the power of sex.
I saw Star Wars VII, so I recognize one of those names. I have no recollection of who General Hux is.
I'm sure there's good fan fiction out there. I personally haven't read any unless we're counting "it's fan fiction because the original author has been dead for almost a century" books.
I agree with you that the "author is dead" is not a valid reason for something to be considered fanfic. I mentioned F.M. Busby's death because since both he and his wife are dead (which is sad because I met them at a convention in the late '80s and they were very nice people), neither could possibly object to what I plan to do about posting an online Hulzein Saga wiki and stories that explore the nooks and crannies of what Busby didn't write about, as well as continuing the series from the final novel (Rebel's Seed). There's so much more to that series, and I really don't understand why nobody else has tackled this. I know I'm not the only fan of that series...
A key problem that any sort of recommendation will come across is that I am absurdly picky over my reading material. Going through the 'free' section on Amazon has led me to 4 good books. I've probably tried at least 60 of them. That's a... bad ratio. For the past couple years I've been almost exclusively reading (licensed) Star Wars books because they've been written by the same core of writers who I mostly enjoy, but even then I've tossed a great deal of them. I think I've read around 90~ books and I started with over 240. I'll likely finish the total stock at a success rate of around 40% which is significantly better than my success rate through Amazon's free ebook service but still abysmally low.
As mentioned, you've barely scratched the surface.
If worse comes to worse... write it yourself. You're an Iron Pen veteran, and I know you can write. It takes time and a great deal of practice, but it's doable. My own first fanfic was terrible - so bad that I'm thankful that only one handwritten copy of that story ever existed, and I sincerely hope the person I gave it to has either lost it or thrown it out. But that was 38 years ago. I've improved since then.
