"Arrivederci, Fiero" Has Ted and Marshall remembering the "100K Fiasco" (althought Marshall insists it's the "Fiero-asco"), Ted and Marshall had to cuddle to keep warm from a snowstorm they were stranded in the middle of the road. Marshall was talking about how he decided that one day he would marry Lily, and then...
Ted: Marshall... Are you still thinking in Lily?
Ted: Please, stop.
"Three Day Rule" is packed with this. There was Ted's fantasy of Marshall and Barney cuddling together in cheerleader outfits, Marshall and Barney on the brink of sexting Ted while pretending to be a girl he likes, and later competing over who Ted would rather sleep with. Not to mention the Ho Yay generator Stan, who has such a good grasp of romantic language that Barney and Marshall nearly fall for him.
Barney: Why do we keep trying to have sex with Ted?
Marshall: I don't know, it's weird.
Season 9 has Lily become crazy jealous after envisioning Robin with a new female best friend. The daydream ends right after Robin and her new BFF decide to have sex.
Then, when she and Robin kiss to snap Barney out of his drunkeness, she is over it and Robin is all Ho Yay.
Marshall when he didn't realize Scooter was Lily's high school boyfriend who was a lunch lady at her school and not a scooter for the lunch ladies.
In the episode "Slap Bet," after Barney tells Marshall that his hand is 'monstrous,' Marshall replies "What did you expect? You've seen my penis."
This extension of a scene in Season 3's "Third Wheel". (@ 3:26)
Barney's Relationship Advice speech to Marshall in "Bagpipes" starts with Barney talking over Marshall's shoulder, and ends with Barney's tongue practically in Marshall's ear while Marshall's eyes are almost completely glazed over. With a running theme in the episode about how hypnotically powerful this speech is to Marshall.
Marshall even has this with a random male from the college he went to with Lily and Ted: "Sweet and cute, but just enough of a jerk so you want to change him"
In "The Perfect Week", Ted slaps Barney's ass reassuringly before he goes to pick up a girl.
Ted and Barney in season 7, when they both get sick of waiting for the right girl and very, very nearly have a child together(well, adopt, but still). They also plan out an entire Heterosexual Life-Partners scenario where they just about draw the line at having three-ways together. This comes straight after a whole conversation wishing they were gay, and talking about how much sex they would have if they were.
Ted's employee at Mosbius Design quits the job and breaks up with Robin at the same time. For those, he brings a bouquet of roses and a letter. He gives the letter to Robin and the roses (plus a heatfelt "I'll miss you") to Ted...
Marshall baby talks to Ted on phone, demonstrating separation anxiety for Kevin.
Ted and Marshall participating at the pregnant course without Lily.
Barney got really close to Ted when grilling him about the laser tag party he thinks Robin's throwing for him. And given the fact that Barney was actually planning an ice party for Robin and Ted was in on this secret, the "grilling" was quite unnecessary, other than just being for show. So why did he feel the need to get that close?