Nanoha's first impression of Fate is "the girl with sad and beautiful eyes," and soon makes it her number one priority to remove that sadness, even at severe detriment to her safety and her quest for the Jewel Seeds. After their last battle against each other, Nanoha gives Fate a Bridal Carry and season one ends with the two embracing after swapping hair ribbons and promising to call the other's name when they need them. They're currently sharing a bed and raising a daughter together, who considers both of them her "mama."
Word of Gay has also come down from the voice actresses for the two characters.
The movie remake of the first season cranked the Les Yay quotient up considerably. Not only was new Les Yay added and existing Les Yay enhanced, but all of the heterosexual Ship Tease moments from the original first season got cut out.
Vivio's found herself in her own Les Yay relationship with Einhart Stratos in ViVid. Inheriting her royal ancestor's bitter regret of failing to protect his beloved rival, the Sankt Kaiser, in the end, Einhart seeks out Vivio... only to learn that she is her own person and not just the Holy Queen reborn. And yet, even though she knows that she's not the Queen she seeks, she still finds herself drawn to her, wishing to meet her again. Meanwhile, Vivio wishes to communicate her true feelings to Einhart and has made it her goal to rise to her expectations and become as strong as the Holy Queen that Einhart remembers through the Hegemon's memories. There's also a semi-canon side story where Einheart asks to try Vivio's home-made cookies, while being clearly embarrassed and Vivio gets very worked up, while trying to make said cookies as delicious as possible, so she wouldn't dislike her.
Hayate "Harem Master" Yagami and...
...Vita. They did the Only One Bed thing before Nanoha and Fate, and Vita spends as much waking time as possible cuddling Hayate. Vita's Nice Hat that Hayate gave to her is her Berserk Button, causing her to unleashing a rocket-drill on Nanoha after she damages it. Hayate only finally snaps once Vita is killed, and after the Wolkenritter are resurrected Vita tearfully glomps Hayate. The manga has Hayate caressing Vita with the latter blushing while they talk about how they like to always live together. The last Sound Stage of the third season has the two of them discussing the events of the Cradle after Hayate playfully tackles Vita into bed.
...Signum. Hayate gropes Signum while she'sasleep, because she knows that Signum would be terribly embarrassed if she did it while she was awake, and Signum is seen holding her in a very compromising position (complete with blushing Hayate) in the artbook. Signum's emotions for Hayate, as understated as they are, are still visibly there in every look.
...Shamal. As Hayate notes in the first A's Sound Stage that she also enjoys being held by Shamal, and when Hayate says that Shamal's breasts feel nice, Shamal giggles with pleasure. At the end of the sound stage, Shamal tucks Hayate in while thinking about her desire to protect her in return for the happiness she's received from her. There's also the scene in A's episode 3 where Hayate gets into a bath with Shamal, and apparently greatly enjoys Shamal scrubbing her leg.
...Reinforce Eins. For the brief time they were together in the prime continuity, the two of them have generated a remarkable amount of Les Yay—from Hayate lovingly cradling Eins' face in her hands to Eins telling her she is "the happiest magical tome in the world" while performing a Heroic Sacrifice to save her and the Knights. Perhaps most blatant of all is the two of them de facto having a child, as Rein Zwei was born from Eins' Linker Core merging with Hayate's.
Teana Lanstar and Subaru Nakajima. Subaru's greatest wish is for her and Teana to always be together forever. Teana is all Tsundere around Subaru, and even their classmates during training school noticed it. Their vacation together screams "Date," complete with a scene where Subaru feeds Teana. When things were looking grim for Teana during the final battle, her thoughts lingered over to her times with Subaru, and she wonders why she was thinking of her then. Then there's the scene where Subaru wakes Teana up by groping her breasts, and The Glomp Subaru gives Teana when they're reunited in Sound Stage X, complete with little hearts floating around Subaru. Subaru even uses "daisuki" (a strong, if ambiguous, Japanese word for love) on Teana, resulting in Teana getting very shocked in the first Striker S Sound Stage X. Subaru generated so much Les Yay that gave rise to the "Rainbows are straighter than Subaru" meme.
Subaru Nakajima and Ixpellia. Ixpellia is very aware of being Really 700 Years Old and Subaru is one of the few human beings she trusts, as the person who pulled her from the darkness of being the King in the Mountain into the new era. She declared that she loved Subaru, before falling unto a Convenient Coma.
Arf's devotion to Fate in season 1 borders on a Bodyguard Crush. When Nanoha tries to befriend Fate and reach out to her, Arf is surprisingly insistent that Fate not listen to her, to the point of seeming jealous. When the TSAB starts pursuing Fate, Arf suggests that the two run away to a place where just the two of them can live together. Near the end, Arf caresses a catatonic Fate's face while suggesting that after everything is over, she will help bring back the Fate that she "loves so much". She also holds an Unbroken Vigil for Fate in episode 8 of the second season, while she is unconscious after having her Linker Core stolen.
And then there's Fate and Signum. In addition to how well those two get along even when they were still enemies, there's also that third Sound Stage in A's, where after hearing how well Fate sings during a karaoke session, Signum approaches Fate and flat out asks her if she could personally sing for her sometime in the future, saying that she loves listening to good songs. As everyone takes note how Signum seems to be in a very good mood, Shamal mentions that "Signum is really fond of Testarossa-chan". Alas, Arf responded by saying that, while Fate likes Signum too, it's not in the same way that she likes Nanoha.
Nanoha and Vita, as Vita often acts in a Tsundere fashion around Nanoha. For example, she offers to help Nanoha out in the third Sound Stage of A's, then gets annoyed when Nanoha pets her on the head, which is repeated in a similar fashion at the end of StrikerS episode 6. Vita is also motivated by a desire to protect Nanoha, almost to the same degree as her desire to protect Hayate, after the incident where Nanoha was injured and nearly crippled while on a mission with her. And then there is the extra chapter in ViVid, which ends with Vita waking up to find Nanoha is Bridal Carrying her to Hayate's house, because she didn't want to wake her up. Her reaction is priceless.
We weren't lying when we said that even Those Two Girls would be involved — in episode 6, once Nanoha starts jumping into the wholeMagical Girl thing, Arisa gets angry that Nanoha's pulling away and thinks that there's something wrong, and desperately wants to know what's going on so that she could be there for Nanoha.
Then Fate shows up, and Arisa starts crushing on her even more blatantly than she crushed on Nanoha in season 1, acting like a total Fangirl. One can only imagine her reaction when she finds out that the two of them are together.
While Lily does look like she is straight for Thoma, she and Isis definitely act very hands-on around each other. Isis' sexuality is still up to debate, though, since (typically for the franchise) she has never displayed any obviously romantic feelings towards anybody yet.
Signum and Agito, post-StrikerS. Agito is the only one who isn't a Wolkenritter, Hayate or Fate who can make Signum smile. She is also the only member of the "Yagami family" who isn't personally devoted to Hayate but, instead, directly to Signum. And she calls Signum "danna", which can mean both "master" and "husband" in Japanese. Bonus points for their relationship having slight D/s undertones: Signum is a dominant woman with a Whip Sword, while Agito wears a collar and a pair of handcuffs in her battle mode.