Brainiac

Final Crisis was raging, but you wouldn't really know it from DC's main line.  Outside of several concurrent miniseries, the ongoing series only had tangential tie-ins branded with things like "Club Dark Side" or "Sightings." 

Action Comics #866

Brainiac part 1 of 5

35 years ago, Brainiac abducts the Kryptonian city of Kandor.  In the present, the Daily Planet has a staff meeting to reintroduce readers to familiar faces, including the return of Cat Grant.  Cat hilariously tells Clark he should get Lasik, adding that surgery has done wonders for her.  He replies that he didn't know she used to wear glasses, and when her advance falls flat she tells him he's from another planet.

After the meeting, Clark changes into Superman to intercept an alien object falling to Earth.  It turns out to be a robot that he mistakes for Brainiac, but after the encounter we see the real Brainiac in his skull-shaped spaceship now heading towards Earth.

Gary Frank joins writer Geoff Johns for another epic that will reinstate previously retconned continuity and change Superman's life.  Although they had both gone through several versions since the Man of Steel reboot, this story would restore Brainiac and the Bottle City of Kandor's pre-Crisis origins.  This issue was loosely branded as a Final Crisis tie-in with the "Sightings" banner, although most of these tie-ins had little if anything to do with Final Crisis.

Superman #676

Superman teams up with Golden Age Green Lantern Alan Scott to stop Solomon Grundy.  This story was originally intended to appear in Superman Confidential, a series that like its companion, Batman Confidential, told stories set in the characters' early years.  Though the period isn't clearly established, the interaction between Lois and Clark reads more like it occurs before Lois knew Superman's secret identity.  Because of the parameters of Superman Confidential, the stories in that series usually didn't have much impact on continuity or character development, and tended to focus more on storytelling.  Despite the last minute change, the Alex Ross cover does in fact depict an actual scene from the interior story where Solomon Grundy strangles the Man of Steel underwater.  

Superman/Batman #49

K part 6 of 6

Superman and Batman's mission to rid the world of Kryptonite leads them to LexCorp's current CEO and Clark's childhood friend, Lana Lang.  Uncharacteristically, Lana claims the pressure of her position won't let her cooperate with them, and she threatens to turn her Kryptonite stockpile into a dirty bomb that will make the Earth uninhabitable for Superman and other Kryptonians.  Superman's unwavering faith in Lana is crushed when she pushes the button.  Fortunately, the young hero Toyman was already prepared to clean up the mess, negotiating with Batman for a date with Power Girl even though he had done the right thing already.  After the clean up, Superman confronts Lana from a safe distance with the stinging words: "Lois would have never pushed that button."  Superman throws all the Kryptonite they've collected into the sun, but he entrusts Batman with the last piece of Kryptonite in the world just in case.  Batman puts it in a safe in the Batcave, where it's revealed he still has a secret stockpile of several varieties of Kryptonite.

Superman's trust in humanity is continually betrayed throughout this story arc, up to the very end when the most bitter betrayal comes from his best friend.  Lana's ruthlessness is starting to push her into irredeemable villain territory, but this turn into villainy wouldn't really be referenced again by future writers.