Clark and Lex in Smallville. Especially in the earlier seasons.
The Ho Yay in Smallville gets kind of funny when you watch the Audio Commentary on the DVDs and realize that the writers/producers not only know what's going on with the subtext, but actually make it intentional. For example, on the audio commentary of the "Pilot" episode, someone actually says "We just like the idea of them kissing here." when Clark gives Lex CPR, and in "Red," someone else brings the viewer's attention to the... very "appreciative" look Lex gives Clark after his wardrobe change. In the Truth commentary, Allison/Chloe mentions how "cute" they look together. Three out of four times, in the audio commentary someone will mention the Ho Yay of Smallville, proving that it's not all in the head of hyperactive fangirls.
This editor heard from one of the writers' own lips (World Con 2006) that she'd been involved in the pre-planning for the show. Asked by the producers "Are the gay sex people going to like it?" she replied, "We are so there."
There's also a rumoured scene in the season 7 finale "Arctic" in which Lois confronts Clark on what was really the motivation behind his and Lex's friendship - asking, "Why would a billionaire become a rugged farm boy's BFF? There had to be more going on than just gratitude." and stating that she was a lot more "open-minded" than one would think from a conservative general's daughter. Unfortunately for the "Clex" fans, the scene was cut - whether this was because of the implications, or because it just didn't gel well with the scene is unknown.
Even after Lex as we know him leaves the show apparently for good,Clex persists: the child clone of Lex in season ten has some of the original Lex's memories. Where do we find him after he runs off? What memories from Lex's life come through? We find him at the loft, remembering all of the sweet bonding moments he had with a certain farm boy, as well as the sense of betrayal for Clark not telling Lex about his powers.
This troper can't tell the episode, but there is a scene where Lionel is in talking in a couch with a Intergang boss and... it just gets a "vibe" that they are going to kiss. Of course, it should be noted that Lionel is played by a gay actor.
Apparently the executive position at Luthorcorp has "hoyay" as a requirement. Tess Mercer's first episode involved an exchange with Lois, who was dressed in a French Maid outfit (as a disguise). Upon exposing Lois, Tess rubbed the front of Lois' frills and said "So you like to play dress-up?" Tess and Lana's meeting follows this pattern as well. And then all the young, hot female assistants Tess keeps around...
This continues in S9. The description of the scene in Episode 2...see for yourself. (She even says she misses the maid's outfit!)
Tess: The last time [she and Lois] saw each other, things did get a little... physical. Didn't they? (shimmies subtly on "physical")
Come S10, the two of them are working on the same side, making the Les Yay even better!
To a lesser extent than with Lois, Tess has it with Chloe as well, especially in the last season.
Cassidy once mentioned she wanted her character to kiss Chloe. That's all.
And in Noir, Clark Kent and Jimmy Olsen are sitting in a bar ( . . . no, this isn't going to be a bar joke). Jimmy Olsen is staring at Lois Lane, who is dancing in a tight dress.
Clark: If that's what you're after, get in line.
Jimmy: No, no, I'm just . . . (He glimpses Lex Luthor, and his head turns, apparently forgetting Lois entirely.)
Clark: Oh, so it's Luthor you're after.
Clark and Bart in Run.
Bart: You know you could come with me.
Clark: Or you could stay.
Bart: You have a great life, Clark, but it's not mine. I have no reason to stay in Smallville.
Clark: You have me.
(Cue tender looks that linger just a few seconds too long.)
Bart: Thanks for being my friend.
Clark: Are you sure there's nothing I can do to change your mind?
Bart: Tell you what. If you can catch me....I'll think about.
Tina Greer, who previously wanted to replace Lana, suddenly, upon her return in the next season, just wants Lana. Which leads to a wonderful (or terrifying) scene of Chloe hitting (that is putting it mildly) on Lana (because, you know, Tina was a shapeshifter).
This was already present in her first appearance: before the part where she tried to replace Lana, she'd wanted to live together with her "like a sister" and generally acted worshipful toward Lana until it became clear she couldn't live with her after all. THEN came the replacement part.
A completely unintentional case comes between Chloe and Alicia in "Pariah", where Alicia's sudden appearance to Chloe followed by a lot of grabbing of her and speaking to her in her low, sultry voice can be easily taken out of context when considering Alicia's Yandere personality and the sheer seduction that she just can't seem to take out of her voice whenever she talks ("It's gonna be OK, Chloe...")
Clark and Zod has quite a bit in Upgrade, with Zod's talk of no one else being their equal. Tess lampshaded it when Chloe finds them alone on the top of a skyscraper.