There's this fanfiction called 'Lily's Discovery'. It's quite interesting as it not only focuses on the moment Lily finds Snape crying but also on what led up to that moment. It gives a backstory about Snape's recent struggles in the Slytherin house and how Lily's discovery might be a turning point in their friendship. It's a must - read for fans of their relationship.
There could be a fanfiction named 'A Moment of Vulnerability'. In this, Lily finds Snape crying in the Potions classroom after a particularly harsh encounter with James Potter. It shows how Snape's pride is broken and Lily's reaction to seeing his vulnerability.
Perhaps she's being bullied. In the wizarding world, there could be other students who pick on her because she's a 'Mudblood'. This could be really distressing for Hermione, and when Snape finds her crying, he might be conflicted between his general dislike for Gryffindors and his sense of justice.
He might be initially startled. Snape is used to seeing Hermione as a strong - willed and confident student. So seeing her crying could catch him off - guard. But then he might quickly put on his usual cold facade and ask her curtly what's wrong.
Socially, it could be difficult for him. If others find out that he still has feelings for Lily and she's pregnant, he could face ridicule or be the subject of gossip. Also, depending on his relationship with Lily's partner, there could be conflict. He may have to face the fact that he has to keep his distance more than ever to avoid causing trouble for Lily and her unborn child.
He might be initially shocked. Snape has deep and complex feelings for Lily. His reaction could range from a moment of stunned silence as he processes the news. He may also feel a pang of jealousy towards the father, whoever that is. Given his love for Lily, he'd probably be very protective in his own way, despite the situation being complicated by their past and his past actions and associations.
One popular fanfiction could be 'The Unseen Bond' where Snape stumbles upon fem Harry crying in the Forbidden Forest. In this story, it delves into the complex relationship between them as Snape is initially shocked but then shows a side of unexpected kindness.
One possible fanfiction could be 'The Unseen Pain'. In this story, Percy might be crying due to the overwhelming pressure of his demigod duties. Nico stumbles upon him in a secluded corner of Camp Half - Blood. Nico, initially hesitant, decides to approach Percy and offer his silent support.
Snape's initial reaction would be one of disbelief. He has his own set of prejudices and ideas, and gay romance fanfiction is far from his realm of understanding. He might snatch the fanfiction away from Harry in a fit of annoyance. But as he sees Harry crying, he might start to wonder what in this strange piece of writing has such an emotional impact on Harry. This could lead to a very awkward and tense moment between them, with Snape not knowing how to handle the situation properly.
I would recommend 'The Cry in the Corridor'. In this fanfiction, fem Harry is crying in a corridor after a particularly difficult encounter with some bullies. Snape finds her and his first reaction is one of annoyance but as he sees her distress, he starts to feel a strange sense of protectiveness. The plot then thickens as it explores how this encounter changes their dynamic in the Hogwarts environment.