At one point music teacher Dewey Largo was caught in a car with Smithers (the show's most obviously gay regular), denying wholeheartedly that they were doing anything other than carpooling.
Lenny and Carl, to the point of it being lampshaded.
Lenny: I can't tell where Carl ends and I begin!
Carl: See, comments like those are why people think we're gay.
Lenny: Even Bart was throwing dough around. He paid me and Carl a thousand bucks to kiss each other.
Carl: Hey, did we ever get that money?
The writers enjoy hinting it such as when the pair were watching Homer and Marge kiss: "Carl remember when we used to kiss like that (beat) with our respective girlfriends?" and also when Homer is organising gay weddings but has run out of clients we get this Crowning Moment of Funny:
Bart: All you can do now is wait for some straight guys to turn.
Homer: Hmm, where are Lenny and Carl?
Marge: Don't you rush those two! That is something they need to work out themselves.
For some other common ones, Homer has the occasional mancrush, including many men that have an interest in Marge.
Nelson also seems to have some issues, and in the episode, "Little Orphan Millie", where Milhouse's parents go missing, Nelson, as well as Bart are a part of the crowd in the school that fawn over Emo Milhouse.
Don't forget Bart and Milhouse in general. Bart even gives him roses in one episode!
They even lampshade it now. In the episode "Postcards from the Wedge", Bart has to get a rectal thermometer check-up from Marge in his bedroom, and Lisa replies "Just close your eyes and think of Milhouse."
In the episode where Apu gets married, Milhouse arbitrarily shows up, and the guys on the commentary track chalk it up to his being Bart's "plus one".
And when thinking of things to make Homer mad so he can have inspiration for his outsider art, Bart says, "Well, I'm flunking math, and the other day, I was a little attracted to Milhouse!"
Also, in "Lisa the Drama Queen", Lisa becomes best friends with Juliet Hobbes, a girl with a British accent who likes roleplaying. And in their fantasy world, they're the two queens who rule over the land of Equalia. And Marge, fearing that their friendship is having a bad effect on Lisa, attempts to separate them. And then they run away together...
This is based on the plot of Heavenly Creatures, which was in turn based on a true story. The girls WERE budding baby lesbians in that incident. And then they killed some people.
Smithers. That is all. Though some viewers will try to handwave this as Single-Target Sexuality (meaning that Smithers isn't really attracted to men or women; he's just attracted to his boss Mr. Burns and gender really doesn't matter).
Homer has also kissed and hugged Ned, filmed him naked in the shower, and Ned puts up with every Jerk Ass thing Homer does.
Skinner and Chalmers have had quite a bit of this in recent years. "We'll have to bite from each end! We'll know we're safe when our lips meet in the middle".
Better yet, the thing they're "biting from each end" is a cake shaped like a penis that crashed into Skinner's house while Chalmers was over for dinner.
In a later episode, Homer and Chief Wiggum develop a friendship that verges on this at times.
In a similar vein, in the episode "Donnie Fatso", Homer teams up with the FBI to infiltrate the mob, and becomes incredibly close to Fat Tony. True, the constant touching, hugging, and kisses on the cheek could be Hand Waved by Tony being an Italian gentleman, but when Tony dies of a heart attack during a sting, Homer mourns like he's just lost the love of his life. It's rather sweet, and a tad suspect. Tony even lampshades their close bond: "To heterosexual male friendship -the kind the Greeks wrote about."
Marge and Lindsey Naegle make out during Homer's daydream in "How the Test Was Won".
There's probably some subtext between Marge and Ruth Powers in "Marge on the Lam", even though both of them aren't 'really' lesbians since Marge is already married to Homer and Ruth is already divorced and willing to look for another man.
There are some amazing Les-Yayish undertones between Marge and Belle (the Burlesque house owner) in Bart After Dark
Then in The Movie, where Ralph Wiggum, after seeing Bart naked, proclaims "I like men now!"
He once referred to Bart as his boyfriend and another time he hugs Comic Books Guy and says he will never let go.
In "Hungry Hungry Homer", while Homer is convincing Sherri to go to a dance with Bart.
Homer: Who would you rather go out with?
Homer: Well, duh! He's breathtaking.
Also, in the episode "Lisa the Tree Hugger".
Homer: This is all your fault, with your non-threatening Bobby Sherman-style good looks! No girl can resist your charm!
Jesse: This was her choice, Mr. Simpson.
Homer: I'm sorry, I wasn't listening, I was lost in your eyes.
In one episode Bart swaps lives with his rich look-alike and during dinner, Milhouse notices Barts' beautiful "half-siblings". He says they're beautiful, but then says just the girl, he didn't notice the beautiful boy. He says with a dreamy look on his face.
There's an episode where Homer meets Karl (no, not that one!). Karl helps him work to the top, writes his speeches for him, then tells Homer he isn't a fool. Why not? Because his mother told him never to kiss a fool— which he does then. Homer also accidentally blurts out "I love you Karl- I mean, Marge" when a singing telegram guy shows up at their door.
On one occasion Homer commented on how attractive another man was and he has been kissed by another man on two separate occasions, and while clearly surprised didn't react negatively either.
Yet another, in "The Haw-Hawed Couple": Bart becomes Nelson's "best friend", and it's played exactly like a relationship, with lines like "I've known him for ages, but we met at a party and hit it off right away" and jealousy over Bart 'flying kites' with another boy. Complete with a Brokeback Mountain homage at the end.
Nelson: Haw! Haw! I touched your heart!
Homer going into fanboy mode over Rainier Wolfcastle. "Oh I love your movies and your powersauce bars and your taut ... rippling ..." Rainier interrupts him before he can finish.
Nelson and Jimbo sure seem to touch a lot whenever they have scenes together.