In the Search for K, Superman falls to his knees in despair when he and Batman found out that the squad armed with krypotonite weapons out for Superman's blood was created and funded by the US government itself (surprisingly Lex Luthor isn't involved). They didn't care about Superman's devotion to protect people and they wanted him dead. Batman then snaps Superman out of it by telling him that he believes in him.
Issue 50, aptly titled "The Fathers", revealed that Superman's father, Jor-El, had met Batman's father, Thomas Wayne. Jor-El explains that Krypton will explode soon, so he is trying to determine which planet would be the best candidate to send his infant son to. He has already interviewed people from several other worlds, and Thomas is the latest one. I will paraphrase this part, since it's been a while since I read this.
Thomas: I have to warn you that Earth people are not perfect. We have a tendency for misusing our gifts for war and personal gain. But I assure you, if I find your son, I will raise him and love him as my own along with my own son. Jor-El: (smile) That's what I was waiting for. (the other candidates had offered knowledge, glory in battle, living like Gods... but never mentioned anything about love)
Later on, Clark and Bruce talk about how Batman relies on the success of Wayne Enterprises, which in turn stems from the technology from the probe Jor-El sent, and how Kal-El would never have been sent to Earth if not for a decent man who found it. Then, in their respective monologues, they think about how the other is the closest thing they have to a brother. Here it is◊.
Issue 76. All of it. Clark is obviously shaken over Bruce's death. Before his funeral, Clark tells Lois that nobody will be wearing uniforms. He doesn't wear his glasses. Then, he thinks about his father, whose death he could not stop it, seemingly blaming himself for Bruce's death, and showing how much he cared about Bruce. But the Crowning Moment of Heartwarming is when he talks to Diana after lashing out at Dick Grayson, who had taken up the mantle of Batman. He says that it's sad how the two will outlive their friends and loved ones, and he questions what he'll become when he's lost too much... Diana can see that he's just trying to rationalise this, and tells him that the truth is, He just misses his friend. Clark then goes to apologise to Dick, and they Bruce Wayne, and how the two were the only ones that truly understood him. Superman says that he and Dick won't always agree. After all, that's what always happens when he works with Batman. Queue manly handshake and Manly Tears from the reader.
In the first arc of the New 52 series, which details their first meeting & working together, Superman & Batman travel to Earth-2. When the Superman & Kents of Earth-2 first meet the Superman of Earth-1, Ma Kent instinctively goes to her son's counterpart & realises that the Kents of Earth-1 already died some time ago, before hugging him when he's barely able to respond to her questioning if that's true.
Much to Earth-2 Superman's amusement, Earth-1 Superman is dumbstruck upon first seeing Wonder Woman.
The back-up in issue 3, which shows the first meeting of Earth-2's Clark & Bruce when they were kids, and how they became lifelong best friends at 8 years old.