Fan-Preferred Couple: The vast majority of readers want Pip and Estella to end up together. Even the adaptations swing heavily in this way. The revised ending, preferred by both Dickens and his friends, is the one used in modern printings of the book, while the original draft is sometimes included as an extra.
Ho Yay: Pip and Herbert. Pip is very fond of Herbert, and Herbert refers to Pip as "my dear Handel", or "my dear boy" throughout the novel. Chapter 50 of the original text, when Herbert is tending to Pip's wounds, is swimming in this, especially at the end.
The way Herbert proposed to Pip to share his business with him and Clara just smelled of a threesome attempt that everyone would've agreed with.
Jerkass Woobie: Miss Havisham. After reading her backstory, her actions when it comes to raising Estella become understandable. And of course, Estella herself due to said upbringing.