Shinichi/Conan and Heiji. Heiji's clear adoration for Shinichi is even more amusing when Shinichi is incredibly grumpy about it. Some of the best examples for this are when Conan demands to know why Heiji is at the same event he's at, and Heiji replies "To be with you," complete with heart mark and everything. Then later on, when Heiji's canon love interest and childhood friend Kazuha is introduced, she mistakes Ran for Shinichi. Apparently, from how much Heiji was talking about him, Kazuha thought he was a girl that Heiji was interested in. She makes a similar mistake later on, when she believes Heiji is having some secret affair when he is actually just talking to Shinichi on the phone.
In the Osaka Serial Murder Case, Heiji is disturbed enough by a recent nightmare of Shinichi dying that he loans Conan the charm Kazuha gave him...and the dream turned out to be completely accurate, and the charm did protect Conan. Literally.
Just look at Heiji's delight when he realizes that Conan is investigating nearby.
In one case, Heiji texts Conan "OK" with a heart made up of smaller heart symbols surrounding it.
Kazuha finally gets up the nerve to confess her feelings to Heiji. But one mention of Shinichi's confession to Ran in London and what does Heiji do? He rushes off to find Conan before she can do so. Poor Kazuha ends up lampshading the Ho Yay:
Kaito KID and Shinichi/Conan, surprisingly. Shinichi is paired with Kaito in fanworks about as often as with Ran (and, according to the tag numbers, almost four times more often than with her on archiveofourown), despite the facts that they canonly know very little about each other and are close to twins. Their relationship is usually based off the fact that they are each other's equals in terms of intelligence, and that they can bond over their respective double lives and having to lie to their loved ones. Also, the reason some fans enjoy KID heists is because of his "no one gets hurt" rule, meaning Conan/Shinichi can stretch his intellect without having to deal with the emotional stress of a dead body - in the absence of therapy, what could be better?
In Movie 14, The Lost Ship in the Sky, Conan and Kaitou Kid are making their way back to the blimp after being thrown off. However, the wind blowing against Kid's glider is about to push them off. Conan tells Kid to release the glider. However, because Kid is holding Conan, he can't reach the switch at his waist. Irritated, Conan tries to press the switch himself. However, it's implied that he ends up going a bit... lower.
In KID's Miraculous Midair Walk, KID says to Conan that he wasn't particularly interested in the gem or Jirokichi's challenge, but rather he "just wanted a duel with (Conan)"
The Latter is actually a mistranslation, as KID said that the jewel wasn't the one he was looking for, and that he was only accepting Jirokichi's challenge.
Makoto Okuda from the Shiragami case was a pretty big fanboy of Shinichi prior to Shinichi’s involvement in the investigation of the mysterious deaths of Makoto’s adoptive parents. Then it switches to what Heiji lampshades as a “hate-crush”. He even got plastic surgery to look like him!
Gin and Shuichi Akai. Akai's codename for Gin is "koibito"/"lover". Gin says that he'd be happy if it turned out that Akai was alive, because then he'd get to kill him again.
There's also Bourbon, AKA Tooru Amuro, who correctly believes Akai is alive, and is determined to find him. To the point where, when he goes to the Kudo Mansion to confront Okiya, he pulls open Okiya's shirt to expose where he thinks a microphone is hidden.
For that matter, a lot of Akai's interactions with Conan during the Clash could be read as flirtatious.
Shuichi Akai and Tooru Amuro AKA Bourbon/ Rei Furuya.
Everything related to them would be counted as spoiler. Just so you know, they have their own official fanbook called Akai & Amuro Secret Archives
In this fanbook, their relationship is stated as 因縁/ inren/ fate.
In Movie 20, The Darkest Nightmare, Akai saves Amuro and Rena from being killed by Gin when they are suspected for being NOC
Also in this movie, there is a fighting scene between Akai and Amuro on top of the ferris wheel, which is pretty much meaningless to the plot but chemistry for them.
As of late 2017, about 2/3 of all "new" Conan yaoi doujinshi are from this single couple, which takes up several shelves to display in major doujinshi stores.
Bourbon and Scotch. The whole reason Amuro was so obsessed with finding Akai was to avenge Scotch's death.
One for Kogoro in Episode 541. The climax of the episode has Kogoro saved Takeoka from committing suicide to join with his wife Mitsuko in death with both of them shouting each other name. Judging from Takeoka's reaction when Kogoro caught his hand along with Ran and Conan expression can make you think of something else. Bonus point for that once again Kogoro solved the case by himself!
Chapter 1020 will probably go down in history as "that chapter where Hattori tried to make out with Kaitou KID." Granted, KID was disguised as Kazuha at the time, but considering the reader has been following KID's internal perspective for the heist, we the reader base are fully aware of what's going on.
Mitsuhiko has blushed quite a few times whenever he is complimented by Conan and clearly looks up a lot to him. The most blatant Ho Yay moments between them is in Chapter 753 where he is one of the person who clung to Conan during an earthquake, an action explicitly repeated by Ayumi and Haibara, two characters who clearly stated / hinted to have romantic feelings for him.
Sonoko constantly drops suggestive remarks about the other girls. In a recent case, she eagerly stated "We'll check you all over! <3" as well as remarking on Sera being in only her underwear with a "on full display! <3".
In episode 727-728 Ran has an Imagine Spot of being left on a beach◊ while Sera and Conan run off during a mystery, her being framed behind a running Sera in a way that is heavily suggestive. While it may be because it reminds her of Shinichi doing the same thing, Sonoko sly asks a flustered Ran if she's fallen for Sera (and doesn't seem too dismayed by the possibility). Of course, see her above statement about Sonoko checking out Sera in her underwear.
The 11th non-serial movie, Jolly Roger in the Deep Azure, creates its own interesting historical fiction with the female pirates Anne Bonny and Mary Read. They fought together, always trusted the other to get their back, and were undyingly loyal to each other to the point that Anne, upon escaping from prison, sent a coded message to Mary and proceeded to spend the rest of her life waiting with a love boat ship she'd prepared for the day when the two of them would set sail together again. She never stopped waiting, not even after Mary died in prison. If that wasn't enough, the movie constantly references the pair with their Jolly Roger/pirate flag design, which incorporates both their signature weapons, "two goddesses", and Sonoko's alluding to them in reference to the Official Couple.
Random Tumblr poster: "that time when Sonoko wrote the school play and made it a sappy love story starring her and Ran"
If you don't mind the Squick from their age difference, then Vermouth's affection for Ran is also worth considering.
While she appreciates both Ran and Shinichi/Conan, it's quite clear that Ran is the one she loves more due to the difference between her nicknames for them: Conan gets "Cool Guy" because Vermouth likes his intelligence, but Ran is her "Angel" because she considers Ran to be the angel that came to save her life in its darkest moment. Further elaborated, in the beginning of the Golden Apple arc, she wondered if God really existed and sadly remarked that "No angel has ever smiled at me, not even once". However, after Ran saved her, she told Yukiko through the phone that she had found her angel.
Also, the ridiculous extent that she's willing to go through to protect Ran. She shoots at Calvados, her own teammate because the latter has been shooting at Ran. And while earlier she has been able to keep her cool, she loses it when Ran appears due to the fear of her possibly being in danger.
After Ran finds out Vermouth's been disguised as Azusa and asks if she is the one who called her "Angel" before, Vermouth doesn't admit nor deny, but just asks Ran not to invade further into this, because she's her treasure. Ran blushes at that.
when he realizes that Conan is investigating nearby.
