Warning: The following contains SPOILERS for The Boys season 2 finale.
The Boys season 2 finale revealed that Homeleander shares an obscure weakness with Superman. This is not surprising, given that Homelander exists as a dark parody of Superman, with all of the powers and none of the morals. However, it was surprising that The Boys thought to target Homelander in a way that turned his powers into a disadvantage, using one of Superman's rarely exploited weaknesses.
Superman is famous for both his powers and his weaknesses, having been so powerful back in the Silver Age of Comics that he almost literally seemed to develop a new power every month. As for his weaknesses, Superman is famous enough that even people who have never read a comic book in their lives can tell you that Superman loses his superpowers in the presence of Kryptonite, a radioactive ore from his home world of Krypton. Homelander is similarly powerful, but doesn't have a corresponding weakness. In fact, apart from being unable to see through zinc with his X-Ray vision, The Boys has yet to reveal Homelander having any known limits to his powers.
This posed a heavy problem for The Boys in season 2 finale, as they found themselves considering the question of how to rescue Ryan Butcher from the cabin where he was being held by Homelander and Stormfront. Distracting Stormfront and developing weapons that could potentially hurt her posed no difficulty, but there was nothing in The Boys' arsenal that could hope to hurt the nigh-invulnerable Homelander. Taking a page from Sun Tzu, who said that you should evade the enemy you could not overcome with force and irritate the enemy that was known to be temperamental, The Boys attacked Homelander indirectly with a sound system employing several dozen VoughtSonic speakers broadcasting a signal at a frequency of 190,000 Hz. This is well above the hearing range of an ordinary human (which tops out at 20,000 Hz on average) but apparently painful and annoying to anyone with super-sensitive hearing like Homelander. The noise hurt Homelander enough to send him out seeking the source of the signal, giving Billy and Becca Butcher the time they needed to retrieve Becca's son.
While not as well known as his weakness to Kryptonite, the fact that Superman's enhanced senses can be overwhelmed is something else that the Man of Steel and Homelander apparently share. While not weaponized to the same degree it was in The Boys, Superman The Movie saw Lex Luthor using a painfully high ultrasonic frequency to get Superman's attention. The movie Man of Steel also showed that a young Clark Kent had problems dealing with loud noise, until he learned how to focus his senses to ignore certain levels of stimuli. However, the best example of Superman being vulnerable to supersonics came in the comic book prequel series based on the Injustice: Gods Among Us game, where Black Canary was able to bring Superman to his knees and make his ears bleed with a point-blank sonic scream.
It will be interesting to see if The Boys season 3 will see the team take down Homelander again with a similar trick, based around the idea that having super senses like Superman can be a vulnerability instead of a boon. It's possible, for example, that Starlight might be able to permanently blind Homelander if he were caught off guard while using his enhanced vision powers. Either way, it seems that another confrontation between the team and Homelander is just a matter of time.