Jeff Nimoy (the writer, story editor and director for the English translation) has stated (joked?) that he wrote Izzy and Tentomon's dialogue together as if they were gay lovers.
Then there's Sora and Mimi, who were awfully...eager to strip off and shower together in one episode.
Tai[chi] and Matt (Yamato). Wrestle-to-the-ground fistfights, hand-holding, and head-cradling have all been seen—the Japanese version even includes a scene where they yank Joe's towel off at a hot springs bath.
And the freaking angelic "arrows of love," with an explicit "like Cupid" comparison, combined with manful hand-holding before their first digimon warp digivolve to Mega level in "Prophecy."
Tai[chi] and Izzy (Koushiro) have a lot of moments too, particularly when Matt's not around.
Adventure 02: When a young Chosen/Digidestined girl begins flirting with Ken, Wormmon becomes very jealous.
Ken and Daisuke/Davis have their moments, too.
When Ken asks to give him some time to think about joining them, Daisuke doesn't get it and acts like he's just been rejected.
It's worth noting that Ken already showed interest in Daisuke when he was the Kaiser (the English dub gives us the glorious line "I love to see you squirm!"), that Daisuke claimed to have heard Ken's heart talking to him, that Ken only manages to defeat his fear of the Dark Ocean and send Demon there after he hears Daisuke's words of encouragement (with Hikari and Miyako lampshading the process), that they engage in so much Say My Name that there's a video on YouTube teaching about Japanese Honorifics using scenes of their relationship as examples...
Nothing about Miyako? The blatant, Utena-inspired flowery fantasies of Mimi, then there's her and Hikari...
Hell, there's even some who see Ho Yay between Takeru and Iori (who are 11 and 9, respectively). Then again, given the "synchronize our hearts" nature of Jogress evolution/DNA-Digivolution, I guess the Ho Yay was completely inevitable.
The very fact that Jogress Evolution only pairs same-gender kids (Daisuke-Ken, Miyako-Hikari, and Takeru-Iori).
What about TK (Takeru) and Ken? In one episode (the one where TK Takes A Level In Badass and rips Ken a new one), this troper sensed a bit of flirting in TK's words, and the fact that they make Ken so flustered.
Oikawa's entire motivation is his suspiciously obsessive friendship with Hiroki Hida.
Digimon Tamers: Henry/Jenrya/Jianliang/WHATEVER to Takato, after talking about their differences in their way of doing things: "...That must be why I like you so much." Granted, this was only in the dub, but it's still noticeable. Oh, and... every single frame of the episode "Kazu and Kenta's Excellent Adventure," a Filler episode starring Those Two Guys.
Heck, in the original version of that episode, Kazu and Kenta actually share an Accidental Kiss.
Fans also like to interpret Renamon's absolute devotion to Rika and their entire relationship as a whole as Les Yay. Even JesuOtaku pointed out in her Digimon retrospective that their way of interacting with one another is reminiscent of lovers.
In Digimon Frontier, the amount of hints of Ho Yay for Takuya/Kouji in the series is shocking. Especially once you read between the lines.
In a rather Squicky case, brothers Kouji and Kouichi from Frontier actually had a scene that was so sappy and beautiful that even their enemy at the time (one of the Royal Knights) had to comment on how beautiful it was (although it's not clear whether said scene was "elaborated" by some in-universe Shipping Goggles).
Kouki is also very keen on defeating Masaru, to say the least. It doesn't help that his colleagues Nanami and Ivan have blatant attractions to Touma and Yoshino respectively.
That's to say nothing of the amount of Les Yay between Yoshino and her partner, Lalamon.
Masaru and Ikuto. It's Masaru who wants to save Ikuto the most. And then Masaru let Ikuto to live with his family for a while, and even have a bath together. Said bath scene later appears in a flashback about how Ikuto is very worried of Masaru.
Digimon Xros Wars: Kiriha really wants Taiki as his underling. The opening screen of one episode even had him looking at drawing of Taiki with "My Taiki" above it.
Then there's Nene and Akari, from episode 23 and beyond. Akari is even the one who gets Nene to first open up and smile. In the manga, we also have this scene between the two of them.
Not to mention Blastmon with both Tactimon and Beelzebmon.
And Shoutmon and Ballistamon.
And the only time MailBirdramon shows strong emotions is when Greymon, his digixrosing partner, falls down a large drop.
Taiki is a bit too enthusiastic whenever Baalmon, and later Beelzemon is on scene.