In Blind the Kyuubi negotiates a deal with Naruto about what he can and can't do when Naruto allows him take over of his body during the month long wait for the 3rd part of the exam before they discuss Naruto's training . This later comes in handy during the fight with Gaara and various other points in the story.
In Kyon: Big Damn Hero, Nagato checks Kyon's wristwatch in one chapter. Later on, it saves his life when he gets shot, turning into an armour... skinsuit... thing.
In the 7th Sea story Homecoming, when her father Owen expresses his uneasiness about his daughter Colleen coming with the family to parley with one of the Sidhe, she just pats her guns, insisting on helping her grandmother Moira hunt down her (Moira's) hated brother. Later on, Colleen willingly shoots her father in cold blood with those same guns when she comes upon Owen trying to help his not-so-sinister-after-all uncle escape.
Manchester Lost: Angelic singing kills demons. Who knew the whole climax was going to hinge on this little bit of trivia?
In Axis Powers Hetalia fanfic Outcast Tino mentions putting a star shaped ornament on Flower-Eggs collar, it turns out it holds Torvald's crystal star.
The Fan Verse, the Travelsverse, is basically one big armoury, with Instrutilus constantly placing guns in advance and using them stories later.
Company0051, a HaloFan Webcomic: Master Chief is staying at the local military camp on Noiosi when he comes across a patch of forest with a large hole in the trees. The Captain tells him it was just a meteor. It was actually a shot-down Covenant starfighter which was carrying an AI.
Test Of Humanity, a Portal 2 fanfic in which GLaDOS implants Wheatley's brain into a human body, has a scene where Wheatley ends up overeating and gains quite a bit of weight. Towards the climax Wheatley's overweight frame ends up being what causes GLaDOS to be defeated since it causes him to be stuck in an exaust pipe blowing up a good portion of the laboratory and tearing her apart.
In the Law & Order: Special Victims Unit fanfic Girls' School, Elliot sees his reflection in the window when he is at a crime scene. He later figures out that the main perp could be identified by searching the pictures of the crime, taken by the main perp's girlfriend, for any reflections in those windows.
The original slash novel Captive Prince is notable for using a lot of those. Especially the earring comes to mind.
In the Death Note fanfic Xanatos, L contacts Matt to help him with the Kira investigation after faking his death. As it turns out, L needed Matt specifically because he was the best person to convince Mello to work with Near, being his closest friend.
In The Immortal Game, it's repeatedly mentioned that the easiest way to defeat a bladecaster is to break their faith in what they're fighting for, which makes them lose control of their blade. We see an example of this about two-thirds of the way through the story, when Sir Unimpressive defeats the Cadet, but in truth, this was setting up for how Twilight defeats Titan during the Final Battle.
In Game Theory, Miyuki finds an ice sphere created by a Jewel Seed. In chapter nine, that orb gets shattered when the TSAB attacks Nanoha and Fate's appartment, ripping a hole in reality and forcing the TSAB to close it, giving Nanoha and Fate time to escape.
Nanoha's recklessness with magic screws things up in a big way during the TSAB's assault on the Garden.
Also, Vesta's possession by a Jewel Seed turns out to be crucial to Precia's plan to revive Alicia.
The zombie animating Jewel Seed is what inspired Precia to create her temporary life-support system for Alicia to use when they travel to Alhazred. And then it turns out that Precia actually used that very Jewel Seed to revive Alicia fully.
This is discussed in the Hannah Montana story I Didn't Sign Up For This. Miley's English professor explains the trope and then Miley uses it
In the Gregg Landsman fanfic Glorious Shotgun Princess , it is used as early as chapter 4, when Kasumi Goto steals a Honey Badger from the San Diego Zoo, names it Checkov, as a direct invoking of the trope. In Chapter eleven, the honey badger turns back up as the final bit to Hock's Humiliation Conga
You Got HaruhiRolled! manages to turn the announcement of a new fanfic into one. In Chapter 56, Haruhi complains to the writer, superstarultra, about a fic he wrote in which she and all her friends are in Fat Camp. Then Chapter 81 rolls around, where the version of Haruhi from that fic appears through a dimensional portal and devours an animate cheesecake that was wreaking havoc.
In the Total Drama story, Legacy, Heather's pregnancy is mentioned thrice in the first chapter but doesn't become important until near the end.
The Powers Of Harmony: More like Chekhov's Location, but Dragon Turtle Lake — which Fluttershy and her Guards visit fairly early in the story — ends up being chosen as a meeting place by Luna after the group is scattered.
During their first fight in Episode 3, Fury Cross manages to wound Rainbow Dash with a small slash on her side, which is referred to several times over the course of the chapter as having not healed. During their rematch, it turns out to be a wrath wound, which has been feeding off of her anger and frustration at him and her friends in order to leech her strength. This allows him to nearly kill him before her friends show up to save her.
In Episode 4's teaser, Rarity collects dew pearls for a dress she's making, as it later turns out, for Fluttershy as a birthday present, which she ends up forgetting about completely due to all the time she's spending with Regal Rule. The realization of this when Sweetie Belle points it out is what triggers her My God, What Have I Done? moment.
The hoof-made wing guards Scootaloo gives Rainbow Dash as a gift just before her flying lesson in Episode 5 are later used as proof by Dash that Scootaloo can do stuff right — when everything else in that episode had convinced her she couldn't — as part of a Rousing Speech that pulls her out of her Despair Event Horizon and allows them to defeat the woebeghoul that was feeding on Scootaloo's despair.