"Swiss Family Phineas" has a brief gag where Perry and Doofenshmirtz get thrown in a BIG laundry... cue costume change, with a wedding dress and tuxedo. Doofenshmirtz is the wife.
And in "Gaming the System", after Doofenshmirtz zaps Perry with the Ball-Gown-inator, he can't stop going on about how elegant Perry looks.
Doofenshmirtz: You know, Perry the Platypus, that dress sort of suits you, if, you know, you just accentuate the positive, as they say... Um... I'm going to stop talking now, I'm moving into a weird area.
Something similar to this happens again in the episode "Giants" where Doof makes an -inator that makes people be wearing just underwear. As well as the obvious fact that he himself is only wearing his underwear during this sequence, when a beam hits Perry, Doof actually tells him that he "pulls it off."
In "Nerds of a Feather" after Doofenshmirtz fails to get his show "Doof and Puss" on the air because he wouldn't let the producer give the platypus a girlfriend, we instead get the show "The Platypus And His Girlfriend", with the girlfriend seeming to play the same role as Doof did in the original show.
Not to mention the smirk on Perry's face when Doofenshmirtz adamantly refuses to give the platypus a girlfriend.
In "Bubble Boys", Doofenshmirtz is revealed to have Perry-print underwear.
It's revealed in "I, Brobot" that Doofenshmirtz gave Perry a key to his apartment.
Perry sometimes acts like the other half of a couple when it comes to Doofenshmirtz doing something for his daughter: helping him even in the most ridiculous plans, even if it involves a potentially dangerous -inator.
In "Ferb Latin", Norm walks through a wall rather than taking the door out of Doof's apartment, and Doofenshmirtz turns to Perry and says "He gets that from you, you know", much like a disapproving parent accusing their partner of teaching their child bad habits.
After a sick Doofenshmirtz ends up falling asleep on the floor after another failed attempt with his new inator, Perry comes up to him and....puts a blanket over him. Awwwww.
In "Mom's in the House", when Doofenshmirtz is duplicating Perry's arms, he mentions on more than one occasion that the arms are rather cute.
When Doofenshmirtz has to retake the (insanely dangerous) Drusselstein driving test in order to renew his license, he asks Perry to hold his hand because being with Perry makes him feel safer.
In "Meapless in Seattle", Perry follows Doofenshmirtz to Seattle, where Doof has been taking regular "excursions". When Peter the Panda shows up (with coffee for Doofenshmirtz), Perry's body language and Doof's excuses come off as a cheating lover trying to deny an affair after being caught.
In the very last shot of "Meapless in Seattle" before the credits, it shows Peter and Perry on what seems to be a date◊.
As the series progresses, Doof, Perry, Norm and Vanessa seem to be forming a very strange blended family. Vanessa seems to treat Perry almost like a second father, and calls Norm her brother.
Perry and Doofenshmirtz's hot dog vs. bratwurst duel in "Backyard Aquarium", particularly when Doof gets slapped in the face (repeatedly) with Perry's wiener.
In "This is Your Backstory" we get to see some of the photos◊ Perry keeps in his wallet. All of them depict Perry having fun with Doofenshmirtz.
In "Happy New Year", the two are dancing◊ with each other. This isn't like "Out of Toon" where they were zapped with a ray that made them dance - they CHOSE to dance with each other.
And now Disney Channel's YouTube has posted this. Yes, that is a Taylor Swift song about a relationship.
In "Lost in Danville" Peter the Panda's nemesis kidnaps Doof because he's jealous that Peter went after him. Doof ends up singing a song about how communicating is vital in relationships.
Buford and Baljeet
Baljeet and Buford's Ho Yay tendencies are second only to Perry and Doof's, especially in the hour long special "Summer Belongs to You" where they get an AlmostSpaghetti Kiss and then dance together in the finale song.
Buford actually breaks up with Baljeet in "Hip Hip Parade" ("You're dead to me!") and spends the rest of the episode with his "new geek" who he eventually dumps and returns to Baljeet.
"I have a life outside of you!", said by both Baljeet to Buford and Doofenshmirtz to Perry.
Buford is often seen carrying Baljeet into Phineas and Ferb's backyard in... questionable ways. A tummy pack for babies and a cat crate are two things that immediately come to mind.
"The Bully Code", where Buford becomes Baljeet's "Slave For Life", and begins doing unnecessary things like handing him toilet paper when he's using the bathroom and going through his underwear drawer.
In their song "Frenemies":
"We both have our roles; this is a symbiotic relation... ship.
The animation sequence for this song, when played without sound, is pretty bromantic.
In the Christmas Special, they're lying in bed together while Baljeet talks about how his one special Christmas wish is getting a kiss under the mistletoe. Buford interprets it as Baljeet wanting a kiss from him, and subsequently runs off.
In The Tri-Stone Area, Bufkar enters Phinebunk and Gerb's yard dragging Baljar behind him by his ankle, and Baljar looks incredibly happy about it. Normally this would be nothing special, except that it's been said that Cavemen used to drag their wives around by their ankles.
There's an episode titled "Bully Bromance Break Up" where Baljeet essentially dumps Buford, angry fight and Baljeet storming out and everything. Seriously.
Not to mention the official episode summary claims that Buford is "heartbroken" over the loss of Baljeet, and to fill the void he becomes evil.
Buford: There comes a time when you realize you don't want to bully everyone. You just want to bully someone you love.
Just GUESS who he's talking about...
Not to mention the song 'Hole in My Heart', where Buford and Baljeet sing about how without the other there's a "Nerd shaped/Bully sized hole in [their] heart." The whole song was played like a couple who had broken up and then realized they still love each other, complete with Baljeet drawing a heart on his chest and Buford ripping a heart-shaped hole into his jacket.
BASICALLY this whole episode was brimming with ho yay.
Carl and Major Monogram have a few questionable moments too... one that sticks out is that whole "bet" thing...
One may question Irving's... "obsession" with Phineas And Ferb. oh, and look at this gem from the Clip Show episode
Phineas: And those who love me right back!
Candace and Stacy. Particular examples include "Canderemy" and "Put That Putter Away", where they end up in bed together.
They've also had their own break-up episode.
Candace and her British cousin Eliza, mainly due to the ending of the episode featuring her where she and Jermey say "That's our girl!" about Candace in unison. There is also this freeze frame bonus◊.
The end of "Quietest Day Ever" when Buford gets hit by the -inator.
Ferb: Have you ever noticed that in a certain light, Buford looks... handsome?
In "Norm Unleashed", Dr. Diminutive stood trial for damage he caused using an Inator stolen from Doofenshmirtz. Doofenshmirtz (who had been called to attend Jury duty), when asked, told the court that he has never met the defendant in his life, to which Diminutive proclaims that he has proof of himself and Doofenshmirtz being friends, using this picture◊ from the 2007 L.O.V.E.M.U.F.F.I.N. Pudding revue, which he had kept in his wallet. As the judge demands order, Doofenshmirtz, clearly at a loss, asks the jury why Diminutive would keep the picture in his wallet. Good question, Doof.
Vanessa and Stacy, following their screentime together in "Druselsteinoween". The fact that they were dressed in the same respective costumes as most of the couples there didn't help.
"Lost In Danville" is almost as blatant as "It's About Time" was when it comes to Foe Yay subtext.
Peter the Pandaís nemesis, who acts very much like a jilted ex-lover, kidnaps Doofenshmirtz in a fit of jealous rage, fully intent on murdering the hypotenuse.
Professor Mystery: Peter the Panda is NOT your nemesis!
Dr. Doofenshmirtz: Ah, youíre right. Heís more of a thwarty call.
Professor Mystery: Donít you diminish him like that!
Dr. Doofenshmirtz ends up giving Professor Mystery nemesis advice during the course of the episode, which sounds remarkably like the sort of advice someone would give to a person having relationship problems.