Barney snogs Marshall in the first episode, just to show he's secure in his heterosexuality.
When Ted gets into a car crash, there is a montage showing the people he loves most. Who pops up the most? Barney. A lot of the visions show him in various states of undress, to boot.
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."
Lampshaded once more by NPH during the Comic Con panel, while bemoaning having to be slapped by Segel: "Have you seen the size of Jason Segel's hands?! They're mitts! They match his penis! It's not fun! Either of them!" (@ 8:50)
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.
Barney got really close to Ted when grilling him about the laser tag party he thinks Robin's throwing for him. 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?
In "Ring Up", Barney insists that he was feeling everything that Ted felt while banging a woman because of a "bro-nnection". Turns out the woman was Barney's half-sister which leads to this realization:
Barney: Now I know why I felt everything you did to her last night! It wasn't a bro-nnection — it was a sis-nnection! Oh my God! Ted, did you (whispers in Ted's ear)?
Ted: (smirks) Big time.
And then later...
Ted: Barney, let me ask you something. Were you, uh, feeling a little sore this morning? Especially... (whispers in Barney's ear)
Barney: (gasps, flushing) FRIENDSHIP OVER!
In "Unfinished", Marshall and Ted suspect Barney as "putting the moves on Ted", a la his flirting technique with women, in order to get Ted to work at the GNB. Marshall says he hopes it's only to get Ted to work there, then backtracks and admits he likes Ted and Barney as a couple. Lily says the same thing later on.
In "The Broath," Barney makes Lily and Robin kiss as an apology to him for meddling in his relationship. After that, he says, "Now the gentlemen-" And Marshall and Ted kiss. He then clarifies: "I was going to say now the gentlemen bump fists. How long you been holding back on that?