Strong Bad: Go away, Strong Sad! The Cheat and I are down here shenanigan-ing each other in the dark alone by ourselves. Strong Sad: Uh, are you sure you wanna go on record with that explanation? Strong Bad: Of course! I don't see how that could possibly be taken out of context! —Homestar Runner, "your edge"
There's plenty of it, and pretty obvious examples too (Brooke Burgess even lampshades in in the commentary track) in Broken Saints between Raimi and Oran. Especially since after the end, the two of them seem to be solid Heterosexual Life-Partners in the most straightforward sense.
They do spend some cuddle time in Raimi's medical fridge. Oran's shirtless too. Yeah, all right, so they were only in there because Oran threw Raimi in with him last-second to avoid being fried by the EMP blast that hit Raimi's apartment. But try telling fangirls that.
Homestar Runner once said that his best friend Pom Pom "hewped me out of some pwetty tight jams, and some pwetty tight pants, awthough that onwy happened once." Also, apparently, Coach Z is Bubs' wife. Most instances of this, however, are between Homestar and Strong Bad, and are typically odd sideways jokes about how strange the idea is since the latter hates the former.
There's also the Strong Bad e-mail do over, in which Strong Bad imagines Homestar (dressed up as The Cheat) falling in love with him.
In different town, Strong Bad imagines Homsar as "a modestly hot girl to get me through the hard times."
In one Halloween cartoon, they go overboard with this, as Homestar refers to (seemingly dead) Pom-Pom as his "best friend and concubine", although he immediately claims he doesn't know what that word means. (Without being prompted by anyone.) He also refers to Strong Bad as "Hunky Strong Bad" every single time he talks to him in this episode, after Strong Bad calls himself that once, and is about to say it one last time when a piece of Strong Bad's costume pokes him in the crotch. (While he's wearing daisy dukes, no less.) He also refers to Strong Bad's "sweet rectangular mouth," and tries to get an inflatable (male pronouned) pumpkin's phone number, as lampshaded by Strong Bad.
Speaking of the holiday, one of the Halloween costume commentary videos includes, as its very last photo, a picture of an attractive woman dressed as Homestar. Upon seeing said costume, Strong Bad declares that his brain is "splitting in half" due to mixed signals... and then Homestar himself shows up, notes that Strong Bad seems tense, offers to give him a back rub, and calls him "sweetie". Strong Bad runs off in a panic, and Homestar notes that he "should probably stop calling everybody 'sweetie'".
This whole vibe used to be more subtle, and kept to a few awkward moments here and there. Bottom 10 and Long Pants both feature Homestar behaving in an awkward, suggestive manner towards Strong Bad, doing a butt dance in the former case, and showing up wearing the daisy dukes in the latter. Although the strangeness of Homestar's behavior in Long Pants goes far beyond the psychosexual.
Furthermore, one of Marzipan's answering machines reveals that Homestar finds Strong Sad's voice attractive; albeit it was when he thought it was Marzipan speaking, but he drops in a "Call Me" to Strong Sad's face long after he apparently realizes his mistake. Conclusion: Homestar is into Anything That Moves.
In Deep Space 69, Jay and Hamilton, as Heterosexual Life-Partners, come off like this at times. In one episode, Jay straight-up flashes his penis to him asking for an opinion like it's a totally normal thing to do, while Hamilton is disgusted. He also seems legitimately attracted to Hamilton's crossdressing in one episode and refers to him as a 'sexy lady'.
Paula in No Evil is introduced in the prequel comic "Judgment" being indifferent to any more boys turning up but enthused about the thought of new girls being added to the group. In the series, she spends a lot of time with Kitty, is seen picnicking with her, knows her well enough to instantly tell that leaving a job unfinished is out of character for her in "Three for a Death", and has even embraced some of Kitty's interests (sewing, for example) that a younger Paula would have rejected as too stereotypically girly. Neither Kitty nor Paula has ever expressed romantic or sexual interest in men. "Kitaula" is one of the more popular ships in the admittedly small fandom, at least on Tumblr.