This list isn’t really a rec list (although they are all great stories and favorites of mine), and it’s certainly not a comprehensive Rejected!Harry list. I have a special weakness for stories where Harry thinks he is being rejected by Severus. Occasionally, he truly is, but this only works for me if there is a happy ending to it. This list is for those scenes where your heart clenches, and you want to cry for Harry as he tries to hold it together, because really, as much as he hopes to be loved, he expects to be rejected. Sort of spoilery as a short description of each scene is given.
Broken Bonds, by diagonalist.
The scene where Harry shows up at Severus’ late one night, and Severus asks if he shouldn’t be asleep. Harry assumes Snape doesn’t want him there.
(also
here)
Dumbledore’s Folly, by DementorDelta.
Harry wakes up after their night together, and Severus has left.
Every Time You Leave, by Mia Ugly.
Snape tells Harry he doesn't want him.
An Eye For an Eye, by Arsenic.
Harry watches Draco and Severus make love, and thinks he is being both punished and pushed aside.
The Fourth Year, by Calligrapy.
Harry is expecting Severus to leave him once he is pardoned.
In the End, by Anise.
Harry thinks that he and Remus are in an exclusive relationship, but arrives at Remus' house to find a stranger opening the door. More a feeling of betrayal than rejection.
Jerusalem, by meri-oddities.
Harry heals Severus, after which Severus tells him he doesn’t want a relationship with Harry.
Learning, by
spark_of_chaos.
Harry spends close to a year training with Snape, and at one point blatantly offers himself to Snape, and is rejected.
Nocturne, by Tira Nog.
Harry thinks that Severus no longer wants him now that he has been cured.
Peer Review, by venivincere.
Harry tries to explain to Severus that it seems as though one day Severus stopped loving him.
Peripheral Vision, by Alexandra Dane.
Severus tells Harry a romantic relationship between them would never work.
Relations, by AuctaSinistra.
Harry makes a pass at Severus, who then stops all interactions with Harry.
Sunrises, by Julia-the-younger.
Snape rejects Harry’s advances, and then proceeds to insult him horribly.