In Vathara's work Embers, the Author's Notes go a long way in explaining why certain things happened the way they did using real life comparisons including the cultures of Arctic tribes, properly translated Chinese names and terms and the psychology behind a character's portrayal.
The fanfiction Awakening opens with the author admitting to having "a morbid fascination with this period and a deep respect for history" and thus writing the fic as realistically as possible. Various chapters end with notes explaining Josef Mengele's experiments on twins during World War 2, how the twins were cared for, and what happened to most of them after.
A Better Class of Criminal features a supervillain with libriomancy which let's the user duplicate magic items from fiction. Each chapter typically ends in a blurb further describing the magic items to appear in the chapter and where they're from.
The author of Hogyoku ex Machina asked her high school readers if they could define tuberculosis without using Wikipedia to determine if Ichigo and friends would reasonably know. She even checked if House airs in Japan to justify Ishida watching the show.
The Black Emperor contains a scene of Kallen's mother recalling how she fell into drug addiction which takes cues from the story of an actual drug addict.
Shepherd Of The Stars features a lot of Codex entries where the author shows off how much work went into researching the different settings. The author generated randomized tech trees for each faction in the story, tracks what technologies they have researched, and even calculated the composition, armaments, and construction costs of the various fleets that are featured. Considering there are currently ten different factions, this translates to an impressive amount of work.
Between Minds (Half-Life and Portal) is packed with this with everything from helicopter specifications to language translations to first aid to building layouts to real-life weapons to cut game material to the actual mechanics of an EMP.
Child of the Storm takes it up a few notches and shows that this part of Nimbus Llewelyn'sSignature Style. The story uses historically accurate Norse titles and foods, drawing on a lot of minor throwaway details from obscure corners of each of the canons and displaying an awareness of basic physics (in chapter 54, Harry is flying on a souped up Firebolt, which, in the interests of fairness, can't exceed its production top speed on the Quidditch Pitch. Harry considers that he'd rather not find out what would happen to him and the broom if he suddenly lost a third of his speed, and skirts the Quidditch pitch).
It also displays awareness of certain political realities - for instance, it is abundantly clear in earlier chapters that Harry feels that he has a very large bone to pick with Odin, and it is repeatedly pointed out to him that Odin is an absolute ruler and cannot/will not accept such levels of defiance in public, even from his grandson. In private, under certain circumstances, he is rather more accommodating and understanding, the implications of Younger than She Looks where an attractive teenage girl is concerned and uses the exploration of consequences of the basic premise (Harry is the son of Thor, who was incarnated as James Potter in his first shot at humility) of the fic as the engine of the plot.
The author behind XSGCOM has an author's notes section after every chapter, where he/she explains from exactly where in the original works every character, plot-twist and gadget in the chapter came. He does the same for Hunted Tribes and New California Dreaming.
Dueling Trigger Finger mixes the actual trading card game with the anime's "logic"—such as spell cards being activated on your opponent's turn and playing defense mode monsters face-up—but relies less on Deus ex Machina for each victor of any given duel to win. A good example is Makoto's duel with Rex where Makoto locks down Rex's Frostosaurus with Blizzard Dragon long enough to play Dragon Shield on Golem Dragon, making it pointless for Rex to attack and then summoning a monster a few turns later powerful enough to wipe out the rest of Rex's life points.
Every hotel, restaurant, new age shop, and strip joint mentioned in Origin Story is an actual location, and all the prices involved are authentic. The writer mentions several times in his notes that he actually called these people up and asked them questions. Of special note were the women who worked in the men's department at Macy's in New York City, who actually had a twenty minute long phone call with the writer in which they described what could be seen outside the store from the window's of their department.
Vigil goes to some lengths explaining how plasma weaponry from XCOM: Enemy Unknown operates and how it interacts with Mass Effect's kinetic barriers, including the important point that plasma, being a state of matter, has mass and is thus affected by gravity. Furthermore, because thermal energy can only be transmitted through a vacuum by radiation instead of more efficient methods like convection or conduction, plasma that doesn't hit something in space is largely ineffective, especially when ships have heat-resistant hulls. As a result, kinetic barriers prove highly effective against plasma. This caused quite a few angry reviews from readers who incorrectly insisted that plasma was just another form of energy and should ignore kinetic barriers altogether. Ironically, Mass Effect: Andromeda would eventually and firmly decide the question: kinetic barriers do block plasma and particle beams.
The medical procedure in the first chapter of Extra Life was researched extensively and is greatly detailed to show it. Author's notes also tend to draw attention to or mention other things researched, including PTSD, therapy methods, timeline details, and Japanese geography and culture.
Forward featured realistic space movement, including how dangerous it is to have unsecured materials when there's no gravity. Later on, small-unit infantry tactics are lovingly described as Jayne evades a gang of professional, military-trained gunmen trying to hunt him down.
Salazar Slytherin in A Year Too Soon refers to various locations by their names in the 10th century such as using Buwayhid Emirates to refer to the area of Kuwait, Iraq, and Iran. Furthermore, his excuse for not wanting muggleborns to attend Hogwarts isn't a random Freudian Excuse but because most muggleborns were commoners and thus both uncultured and illiterate. Also, many of them were christian and therefore believed magic to be the work of Satan.
One of the reasons the fan blog Brainbent is so popular with fans is because of how accurately and sympathetically it portrays people with mental health issues (except John, who's disorder is unspecified). In particular, Autistic readers really like the non-stereotyped portrayal of Autism.
Pacific: World War II U.S. Navy Shipgirls has the author(s) doing a LOT of research into everything related to each of the ship girls they've created, such as the ship's namesake, how it sank, etc. and integrating these things into each of their designs and personalities. The creators have given anecdotes of allegedly receiving praise from veterans or their family for successfully capturing all these details, although some are so obscure that it goes straight into Viewers Are Geniuses.
In Concerning a Drifter, this is mentioned in an authoress note for Chapter 12 (where we find out Ryuuko is a mother that she wanted know to know if one could find out if the mother had twins (or, rather, if the babies came from the same pregnancy) through via a DNA test, mentioning that she did some research that boiled down to it being "yes and no" with differing reasons, so, to make it more plausible she changed it to where a mistake was made in during the testing.
Also, in said note, she does mention how she did research on Japan's legal systems in regards to rape and sexual assault, mentioning a few outlines on what's considered resistance against the attacker (i.e fighting back physically vs saying "No") and what whether or not if the victim knew the attacker meant to the case and the police asking Satsuki questions about Ryuuko prior to what happened to her and after, even linking to her sources, one of which details someone else's experiences (which did involve similar questions that Satsuki was asked).
In terms of Ryuuko, being kidnapped, held captive, and raped (subsequently being four times impregnated, carrying two babies to term and miscarrying two) for four years can and, a good chunk of the time, do have near irreversible effects on the psyche, however, they might not be to the effect of Ryuuko's. Likewise, what her captors and accomplices did to her could have lasting physical repercussions, as well as psychological ones, as its mentioned that she might need a reconstruction of her private parts and female organs because of the damage she took, along with having her pelvis fractured many times.
From Chapter 18, this is played with. According to the note, she tried to do as much research as she could on the subject of adoption and child custody in Japan, however, she didn't turn up much anything, so she had to "wing it" for the plotline but, if she obtains more info, she'd update her note with her sources. In Satsuki's case, this is a bit more overt, as "takatsubo" is an actual condition, generally caused by a sudden shock of emotional stress.
When writing Cellar Secrets, the authoress did as much research as she could on the subject, as would be noted on the "Wild Child" page, feral children are rare, thus factual information on them is scant, nevertheless, she did turn to two well known cases, Genie and Oxana Malaya, , though mostly the former.
To be more specific, the older Ryuuko is, the less they can actually reclaim what was lost to abuse, neglect, and severe isolation like Genie, who was about 12 or 13 when she was rescued), however, at least, she's learned language due to living around it, even if she didn't have normal human interaction (like Oxana, who lived around dogs but otherwise not away from other humans).
This was probably accidental but The Crimson Garment is pretty accurate with what can be the effects of prolonged abuse in terms of Satsuki's psyche, considering the fact that she associates touch with domination, not being able to tell love from manipulation, and is quite afraid of her mother, along with blaming herself for the abuse.
Wings of Change goes into a fair amount of detail about wing structures, such as having minute receptors on the wings and a large collection of bones, justifying how Meta Knight (and later Kirby) can fly, with the species' powerful lungs also helping them out. It also discusses the actual processes of flying such as needing a high lift-to-drag ratio which reduces the amount of energy needed for sustained flight.
The Daredevil two-part fanfic Marci Stahl is Better Than You does something very few works involving blind people do, and acknowledges that Braille has a number of weird contractions that don't translate well into written English; not just used to combine two words, but also to condense common words into a few Braille dots (and primarily prepositions). It is the discovery of such contractions in the dossier on Fisk that leads Marci to suspect Matt is the Devil of Hell's Kitchen.
The Pieces Lie Where They Fell: The author and his beta/co-writer don't just rely on online translations for the Bilingual Bonuses. They find people who actually know the language they're using.
In Equestria: A History Revealed, the author clearly has done some research into the show and the franchise as a whole. Little in-jokes from the fanbase are prevalent in the fic, and most impressively, the author manages to tie in even the most obscure sources to create one unified Equestrian history canon, pulling from the show, comics, and even the often-forgotten chapter books.
Silent Knight: Nightfyre's flightsuit puts constant pressure on her limbs, ensuring proper blood-flow to the brain during stressful maneuvers. This is the same way real life flightsuits work for jet and fighter pilots.
In the same chapter, Ash Coat notes some materials on the human sword that genuinely act as absurdly sharp material when treated correctly; it's suggested that some Applied Phlebotinum is employed to sustain this condition.
"Celestia Sleeps In" and its sequel "Onto The Pony Planet" by Admiral Biscuit (link) has a blog post for every chapter detailing all the research the author has put into it. This ranges from historical 18th century technology to social mores to anthropology to physics to even actually preparing Equestrian foods in real life to see how the author's human digestive system handles them.
Friendship is Optimal has a lot of accurate science, and the author has clearly done a lot of research on artificial intelligence and philosophy.
Breech Loader, author of fanfiction Prison Island Break, has put considerable research into such things as medical procedures, prison etiquette, blood types, speech impediments, and the kinds of injuries that would really be caused by the weapons used in the story.
The story is also commended for maintaining the personalities of the canon characters even with regard to other canon characters they'd never interact with in canon.
A Changed World suggests that black holes are scary enough without needing to be unrealistic. Gravitational Time Dilation and redshifting of EM radiation, and the interference caused by radiation from the accretion disk are all plot points. The only concessions to Star Trek are natural consequences of Treknology: a ship can use its warp drive to partially counteract Time Dilation for itself (the ships USS Bajor rescues suffered drive damage and couldn't), and can withstand the gravity well with its structural integrity field.
In his first story, Legacy, this is most apparent in the details related to the victim's wound. His later stories have substantial Notes sections that explain the more obscure allusions, among other things.
His Season 1 reimagining story, The Legend of Total Drama Island tends to show his work in-story for such things as inventive solutions to certain problems, and the effects and treatment of hypothermia.
A lot of details went into the researching behind the locations, schools and universities that appear in the real-world AUFreefall, as well as the symptoms of leukaemia, which a main character is diagnosed with early in the plotline.