Colbert: That was you? I thought that was the guy from Ed! Stewart: ... Colbert: 'Cos that guy's pretty cute!
Stephen once did a rather long joke (starts at 4:03), telling the story of how he once seduced and was in a relationship with a gay Jewish man (named Jonathan) for years, only to dump him, as part of a plot to rid the world of gays who were willing to get married. He ended the tale in tears, saying "What have I done?" Saved marriage, that's what.
Then there is whatever is going on between Jon Stewart and Brian Williams whenever the latter is a guest. Same with whenever Denis Leary is on.
"Stephen"/Tom Hanks is also canon. They kissed and declared their love for each other.
In A Colbert Christmas, Stephen Colbert had almost all the guests (which of course included Toby Keith, Jon Stewart, and a guy in a bear suit) under the mistletoe at the ends of their respective songs. "Well, this is awkward..."
Notably, after Stewart left they both looked at each other and pressed their hands together yearningly through the glass of the door for a long moment. It's more than likely that they are fully aware of the subtext.
Fully aware? At this point, they're actively encouraging it.
Recently in an interview with Jon Hamm, Jon (Stewart) told Hamm that if his wife gave him a free pass to have sex with anyone, he would choose Hamm. Later in the same interview he told Hamm he hoped the man was an alien, because "that kind of handsome, it's just not right."
Or the bit in the introduction to the 2006 Oscars ceremony where Jon wakes up in bed next to George Clooney, and then does a happy dance when George tells him it's not a dream?
Stewart and Will Ferrell apparently have a manchild together. Not a lovechild, because it wasn't love...
Jon: (sotto voce) But it was good.
Will: It was forceful! It was against someone's will—
(Jon raises a hand)
"The White House Beer Simulation" sequence had Jon and Wyatt Cenac dancing and groping each other.
In the old 'Even Stevphen' segments that Steve Carell and Stephen Colbert used to do when both were correspondents on the show, they had a Slap-Slap-Kiss variation on this; in one segment, a vicious on-air fight saw Carell suggest that they 'commentate with other people for a while', to which Colbert reacted as if Carell had suggested they get a divorce:
Stephen Colbert: You've been commentating with Robert Novak, haven't you?!