The opening sequence introducing Masayoshi and Goto, their first meeting and almost all of their interactions between each other in the whole series led fans to believe that this could've shift into the yaoi genre anytime. The fact that Goto already got a girlfriend doesn't help.
Up to Eleven when you noticed Masayoshi's clingy attitude towards Goto and the latter's being constantly worrying and protective towards the former. Masayoshi even mentioned that Goto is his only friend and the first one to discover his secret.
Then it's revealed that Goto didn't have any friends either.
Even Mari could see the tension going on between both of the boys, she assumed that Goto is in love with Masayoshi!
She also showed concern for Goto when Masayoshi left to battle Alien Flamenco in episode 18, asking him if he was okay with Masayoshi potentially never coming back.
Another shipping fuel: Masayoshi and Goto joining forces on defeating Guillotine Gorilla.
In Episode 12, Masayoshi visits Goto in his apartment. He looks at him so fondly that Goto is creeped out at first. Later Masayoshi admits that even though he is a respected hero and has true allies in fighting crime now, he almost depended on Goto again.
Goto was the first on Masayoshi's list of people to save from the From Beyond threat.
Masayoshi even included Goto's girlfriend in the list — someone he's never seen before, but he knows is important to Goto. Of course by then he didn't know she was long gone.
Episode 13 gives us a scene where Goto and Masayoshi both look at each other's contact info on their cells and then decide not to call the other, complete with some sad music playing in the background.
Official art features Goto trying to feed heart-shaped chocolate to Masayoshi. Yes, really.◊
In episode 18 Goto stays in one spot all night waiting for Masayoshi, and he even starts chain-smoking because he's so worried.
And what does Masayoshi think of, while he's lying on top of the Moon, on the verge of death? "Goto... I did it."
In episode 19, Masayoshi can't seem to fathom the thought that Goto might have plans that don't include him. Later, after the truth about Goto's girlfriend is revealed, Masayoshi is visibly distressed and very upset that while he's been asking Goto for help from the very beginning, he never paused to think that maybe Goto was the one who needed help.
Also, by the beginning of the episode, Masayoshi has saved the whole universe, met God, and can possibly become the president of the world. He's very excited and can't stop talking about... Goto being happy for finally meeting his girlfriend.
In episode 20, Sawada Haiji threatens to kill Goto to make Masayoshi take on his Samurai Flamenco persona again. What's Masayoshi's response? "If you do that, I'll kill you!" Not only is Goto Masayoshi's weak point, but this is the first time Masayoshi has ever threatened violence on someone.
The plot of the entire episode is Masayoshi needing to discover the meaning of love. It's definitely purposeful.
Case in point: whenever a scene ends in Masayoshi thinking about love, the camera then cuts to Goto.
Masayoshi proposes marriage to Goto in episode 22, proclaiming that he'll work hard to take Goto's girlfriend's place and that he wants to take care of him from now on (all while stark naked!), followed by him finally realizing that that is what love is.
And then there's the entire reason as to why Masayoshi proposed in the first place. He knows that Goto feels utterly alone now that Haiji has deleted the last real text from Goto's girlfriend, and wants to make sure that Goto is never alone again. And while he's telling Goto this, he comes to realize his own feelings.
The scene progresses to Goto calling Masayoshi a virgin, Masayoshi saying "Y-you aren't a virgin?" (implying that yes, he has thought about whether or not Goto is a virgin), complete with a Luminescent Blush, and ends with Masayoshi screaming about how stupid Goto is, which is finally what gets Goto to calm down, calling Masayoshi a freak in a very endearing tone. As Masayoshi is approaching Goto in relief, Sawada says "Love?" but Mari interrupts the scene. When the camera finally shows Masayoshi again it looks like he's pulling back from a Big Damn Kiss with Goto, and given the events that just occurred it seems most likely that this, or even just a hug, happened while the camera was focused on Mari.
Masayoshi asking Goto to marry him, and thereby letting him know he's not alone, is what finally lets Goto say goodbye to his girlfriend and begin to let her go, if the text he lets Masayoshi see is any indication.
And while we don't get to see Goto's reply, by the end "his girlfriend" is a penpal in Nicaragua...
Masayoshi responds jealously to this, but it's also a heart warming moment, showing us that Goto is finally letting go and moving on. The entire scene could also be read as though the two were dating.
BONUS: He never did say no to Masayoshi's proposal; just called him "baka" a few times.
And then there's the song playing during that scene, Makaroon Days.
As we hesitate to hold hands in public, if you told me you loved me now I'm sure I'd respond with a 'yes'
Considering how loaded with hints and subtext the lyrics are for the rest of the music in the show, there's no way this wasn't intentional.
And on top of everything, the song was heavily edited for that scene. There was even another verse in-between which got cut. The lyrics are definitely meant to fit.
It's made pretty clear by the end of the episode that Masayoshi has romantic feelings for Goto. Whether or not Goto reciprocates Masayoshi's feelings is left ambiguous, but considering that the lyrics in most of the songs in Samurai Flamenco are related/pertaining to Goto, and considering the above lyrics in Makaroon Days, the conclusion can be drawn that he does love Masayoshi back.
Actually, if you rewatch the show, around the Flamengers arc it becomes pretty apparent that Masayoshi is quite taken by Goto. (Even if he himself doesn't realize it. His facial expressions say it all.)
Depressing as it is, the fact that Goto doesn't have a girlfriend after all and is in an unhealthy relationship with himself raises the possibility of an eventual BL end considerably.
Goto's girlfriend complained more than once about Goto talking about Masayoshi all the time, and that she felt he has taken Goto from her. This is pretty suspicious by itself, but then it turns out it was Goto himself sending those texts. Let that sink in for a moment.
What is particularly glaring about this is that "Goto's girlfriend" was jealous and felt left aside because of Masayoshi, but when Mari stays in Goto's apartment, "she" is perfectly okay with it and knows nothing will come out of it. "She" felt more threatened by Goto hanging out with a friend than by another woman living with him?
Goto's girlfriend is described as "cute, bubbly, and cheerful". Sounds like someone else we know, doesn't it?.
The Another Days manga is a different can of worms. Since it's set at the beginning of the anime, there are a lot of Masayoshi and Goto moments. Some of the dialogue runs on Double Entendre, such as Masayoshi telling Goto to "take responsability"... because he ate his Limited Edition curry.
Later in the manga it's revealed that Goto and Masayoshi are living together post-anime, if only temporarily.
The mobile card game actually has them getting married◊ in two of the last cards to be released. Needless to say, there was a lot of rejoicing within the fanbase.
The first Character Talk CD does nothing but add even more fuel to the Ho Yay.
Goto says that a 4-5 year age gap at most in a relationship is okay. Goto is 24 and Masayoshi is 19-20.
Mari asks Goto which of them four (Flamenco Girls and Masayoshi) he would take to a deserted island. He replies that of course, he'd only take Samurai Flamenco. Mari proceeds to state the obvious:
Mari: Thereís three girls here, why would you take a guy? Ö Ah! ÖHmmm?
Goto: Donít ĎAh!í me. Donít imagine weird things. If I picked a girl here, there would be too much trouble.
Mari pressing an iPod to the breasts of Mizuki and randomly kissing Moe. Mizuki pretty much states that this is a frequent event.
Episode 10 confirms what we already know in a heartbreaking manner: while Moe would gladly give up her life for Mari, stating "Mari-san is my reason for living", Mari doesn't feel the same. Moe knows this, but it doesn't stop her from trying to save Mari anyways. Also doubles as a Tear Jerker moment when we see the expression◊ on Moe's face.
It keeps getting worse for Moe as of episodes 14 and 15, as Mari flat out explodes in anger upon seeing her again, bringing her to tears.
In Episode 16, the conflict between the MMM girls ends in Mari and Moe passionately making out, and targeting Mizuki afterwards (they run to her, the scene cuts to black, and a smooch sound is heard).
In Episode 19, Mari tries to kiss Mizuki, but the latter wasn't too enthusiastic with the idea.
No Yay: Masayoshi and Kaname, especially in episode 3.