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:
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.
Doubles as Foe Yay: 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.
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!
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.