SPOILER WARNING: The following article contains major spoilers for The Man of Steel #3 by Brian Michael Bendis, Ryan Sook, Jason Fabok, Wade Von Grawbadger and Alex Sinclair, on sale now.
Superman has more weaknesses than just a terrible allergic ration to Kryptonite, or being reduced to less than a mere mortal in the face of magic. There are two major routes to take if you were in the business of making Kal-El emotionally buckle at the knees, and neither one is related to brute strength (although, some heavy hitters have proven this is also an option). Superman lives simultaneously in two different realms in his day-to-day life. One of those is his human alter ego Clark Kent, the reporter and family man. Attacking this facet of The Man of Steel is pretty direct, which is to threaten his family and his livelihood. This is something just about every comic reader can relate to. We all have family and friends we care about (hopefully) and someone putting them in harm's way is soul-crushing.
But the other way to get Big Blue to shed some tears via emotional terrorism is to attack his origins, specifically, any remnant of his dead home world, Krypton.
The relationship Superman has with Krypton is a complex one. Though he was born there, it's a world that he has never stepped foot on in the primary DC continuity (aside from a recent time-travleing adventure alongside Booster Gold), but he feels a deep connection with it nonetheless. Unlike most people who have left their homeland, Superman can never go back, can never visit where he came from. There’s a certain level of angst and loneliness this realization inflicts upon him.
Even when remnants from Krypton are discovered, be it a long-lost cousin or villains from his Krypton, they can’t possibly fill the void of never really knowing what it was like to call his birth place home. This make whatever tiny bit of Krypton (that aren’t built to kill him) Superman comes across deathly important to him. The pinnacle of these home world keepsakes is Kandor, the shrunken capital city of Krypton Superman hides in the Fortress of Solitude.