There's plenty of Ho Yay/Les Yay subtext in the Fire Emblem games, most notably with Florina/Lyn (Blazing Sword) and Ike/Soren (Path of Radiance). Due to the emphasis on Relationship Values to build trust between comrades, anyone can theoretically be paired with anyone. Yes, even Oliver/Reyson, although that's... not exactly stretching it...
Also Legault/Heath. Legault is probably as close as a Fire Emblem character is going to get to out-and-out Bi, but it's most overt with Heath.
Nino from Blazing Sword has some Romantic Two-Girl Friendship vibes with Rebecca and Florina. Who have some RTGF subtext among themselves, too.
And what about Rebecca's hero worship of Louise the Lady of Violets? Including pretty much drooling over her for being so beautiful, ladylike and strong?
Discussed in Radiant Dawn; early on Micaiah mocks Sothe's hero-worship of Ike, describing the latter as "'hero' of the Crimean Liberation, leader of the Greil Mercanaries, and father of Sothe's children..."
Just about everything Heather says in Radiant Dawn is a come-on toward another girl. It's even more blatant in the Japanese version, but the localization team in charge of hiding wasn't trying very hard.
It's a tradition among Fire Emblem yaoi fangirls to slash the red knight and the green knight. From Kieran/Oscar in "Path of Radiance" to Kent/Sain in "Blazing Sword", all the way back to Cain/Abel in the very first Fire Emblem, it can't be avoided. (Until Awakening just made red/green a het pairing, that is.)
Some of them are significantly more slashy towards each other than others. Kent and Sain, for example, have paired endings with other female characters, and even in-story, outside of supports, Kent has a Bodyguard Crush on Lyn and Sain is a Handsome Lech. Oscar and Kieran, on the other hand, don't seem to show interest in female characters: Kieran is obsessed with Oscar, and Oscar, while initially dismissive, grows friendlier towards Kieran, even giving him a special skill scroll in a base conversation in Radiant Dawn because Kieran has the tendency to hurt himself while practicing. D'aww!
Considering that all of Kieran's A rank support consist of him saying he wants to fight together with someone forever, complete with several awkward pauses centered around "fight" and "together," it starts to sound like he's coming on to everyone.
What about Tibarn "tying Reyson to the bed"? Not only that, there's also a bunch of little hints between the two.
"Tibarn, I...owe you my life. You took me in, made me a part of your family... I owe you so much. No matter what happens in this war, I will stay by your side, be it in body or in spirit."
In Sacred Stones: Ephraim/Lyon, and Eirika/L'Arachel are the biggest ones with Lyon telling Ephraim how he simultaneously loved and hated him and L'Arachel compliments Eirika's beauty as much as she talks about herself.
Eirika's not just limited to L'Arachel, either; she has her fair share of Les Yay with childhood friend Tana as well. At the very least, she has a Romantic Two-Girl Friendship going with both.
Also, if you get an A support between Gerik and Joshua, Gerik follows Joshua to Jehanna and serves him for the rest of his life because he is impressed by his swordplay.
While it's innocuous enough, Gerik also takes Saleh out to dinner. He does no such thing for Tethys or Marisa, his female supports.
There's also Artur and Joshua's supports, in which Joshua, as payment for a coin flip he wins, gets Artur to do some late night training sessions with him. All of which occur offscreen. In their B, a big deal is made over whether Joshua is "exhausting [Artur] in training." And at the end of their A, Joshua says, "I want you to keep being my partner."
Speaking of Tethys and Marisa, while their A support is primarily just good-natured teasing, sometimes it really sounds like Tethys was slipping in some under-the-radar flirting...
Tethys: What an interesting reaction. Youth is so cute.
Marisa: Wh-why are you smiling?! Ah...
Tethys: Don't be so embarrassed. We're going to be around each other for a long time. We should talk.
Marisa also goes through a serious Defrosting Ice Queen routine with Tana. And Tana mentions that she "doesn't know what she would do" if Marisa said no to being friends with her.
While theoretically "anyone can be paired with anyone," only certain couples get paired endings, and that's usually pretty telling. A pretty obvious example is Ike in Radiant Dawn: despite Ship Tease throughout all of Path of Radiance between him and Elincia, he has paired endings with two characters, neither of whom are her, both of whom are male.
The fortune telling in Awakening gives us a look into the hearts (minds?) of various characters you have supporting each other, with hearts going back and forth between them if they wanna make babies...even if they can't. The fortune teller is a Scrappy for mocking this, asking two male characters what they're thinking (they're both men!) and considers Les Yay to be a "rather extreme friendship". He's significantly more tolerant(and zany)in the English script, however.
Virion and Libra's supports have Virion gush a lot about how delicately beautiful Libra is. Towards the end, Virion switches gears to praising how much of a Hunk he is, but his comments are no less appreciative in nature.
Maribelle is a bit too fond of Lissa for them to just be "girl friends".
Sumia and Cordelia's supports get to the point where one could easily see them going S.
Tharja is utterly obsessed with the Avatar, and will pine over you nonstop even during supports with other characters. Even if you're a woman. It seems that Awakening decided to make up for all of the Ho Yay in Path of Radiance and Radiant Dawn by heaping on the Les Yay this time around.
Gregor and the Male!Avatar's C support has Gregor offering to tell Robin a secret only men can do. It involves suggesting the Avatar to sleep with him, though in a literal sense, in order to share body heat. The Japanese version of the conversation has Gregor telling the Avatar that he knows a great secret for sleeping together that way. Their B Support has the Avatar flustered at the sight of him because he had a dream involving the Avatar resting his head on Gregor's lap. Gregor notes that his charm hasn't affected another man before.
Inigo and Genome's support while it's obvious that Inigo is referring to going out with other chicks, its easily taken out of context as talking to Genome instead of the girls. Also, in the A support, Inigo cries about wanting to be "manhandled".
The "Harvest Scramble" DLC map, being centered specifically around conversations between characters of the same sex, is an absolute goldmine of this. To wit:
Inigo swipes Gerome's mask of his face and notes he can't see why he wears it as Gerome is very handsome.
Then their one between Donnel and Stahl. After telling Donnel about his old flame that spent the last festival dancing with his friend Donnel offers to dresses like a girl and dance with him in order for Stahl to get out his old "frustrations." Prior to that Donnel did tell Stahl he was a handsome man and he probably was a hit with the ladies.
Another for Gregor who dresses up Ricken like a girl and pretends to be dating him to get another crazy girl off his back. Gregor constantly tells Ricken that he looks cute for a girl and wants to dance with him.
Kjelle downs a shady drink, thinking it to be a strength potion. She ends up drunkenly complimenting Severa on her looks and groping at her clothes. The best part is, that wasn't an alcoholic drink. It was a truth potion.
Kjelle and Lucina deciding to spend the day together at the feast isn't suspicious, even with Kjelle's strange obsession with Lucina. What might be more interesting is that they decide to call it a date. Additionally, this is also unchanged if they're sisters.
Maribelle and Lissa...why don't you judge for yourself?
Maribelle: Hogwash! You are MINE and mine alone, and I am SICK and tired of sharing you!
Nowi feels up Tharja in her sleep after talking about her "boingy bits".
In The Future Past 3, Grima in the body of MU says that the last owner of their body loved Chrom. They say this even if you have a male MU.
The Hubba Tester is a really weird example, since his readings are as likely to confirm whatever theories one might have about the character relations as they are to shoot them down, since the readings are random. Nontheless, it can create interesting results. Doubles as a potential source for Incest Yay Shipping for those that are into that.
It has been commented on in the fan base that the relationship between Chrom and the male Avatar is on par with that of Ike and Soren. If the dialogue from the male avatar's supports were transplanted to the female avatar's, the S support would still make perfect sense. It really drives the point home when both Chrom and the Avatar state they are "Two halves of the same whole."