Ghost Plots are aspects of a story which are altered or omitted from a book before it goes to print.
J. K. Rowling used the term 'Ghost Plots' for the stories that never mentioned or yet published in any books. JKR indicated that Ghost Plots tended to be "superfluous to requirements" "had to be sacrificed for the bigger story". Thus, Ghost Plots tended to be more peripheral or tangential to the story making them a hindrance to a tighter more focused plot. Sometimes JKR originally had two characters playing the same role making one of them redundant.
Some Ghost Plots were removed quite early in writing process, while others were removed later (as indicated when JKR accidentally gave details of ghost plots in answer to fan questions). It is possible that some of what appear to be red herrings  were remnants of ghost plots removed further along the writing process.
Known Ghost plots
- Dean Thomas's father: JKR originally planned for Dean Thomas to find out about his biological father being a wizard, why he left and why he was killed. In Harry Potter and the Deathly Hallows, Dean mentions that his biological father left when he was young and that he does not know whether his father was a muggle or a wizard. JKR said that she sacrificed Dean's backstory for Neville's - though what we know of Neville's backstory seems to have been known by Neville all along.
- Arthur Weasley's death: The family dynamics would have been different and actions and words attributed to Arthur in later books would have to have been said or done by someone else (or omitted altogether) if JKR had gone ahead with her original plan to kill Arthur off.
- Pyrites: His role in the Potters' betrayal / deaths was likely filled by other characters with more of a role in the story.
- Mafalda the Weasley cousin: Mafalda was very intelligent with the sort of belligerence common in Slytherin members such as Draco Malfoy and Pansy Parkinson. JKR said she was dropped because Rita Skeeter did a better job of providing necessary information and having both characters was redundant.
- Florean Fortescue: JKR admits that Florean's presence in Harry Potter and the Prisoner of Azkaban was originally meant to set up a subplot where Harry later turns to Florean for information in Harry Potter and the Deathly Hallows. However, JKR subsequently decided to use Phineas Nigellus Black and Helena Ravenclaw instead to pass on this information. 
- Garrick Ollivander: being the product of a wizarding father and muggle-born mother. Garrick's parentage is hinted at when he knows all about the elder wand and wandlore but nothing about The Tale of the Three Brothers and other fairy tales unfamiliar to muggles and muggle-borns.
- Hermione Granger's sister: A younger muggle sibling which JK Rowling never got around to introducing.
- Garrick Ollivander's mother: Whose muggle-born blood status was only hinted in the books when Garrick Ollivander seemed to know all about the The Elder Wand while drawing a blank when Harry mentioned Beedle the Bard's story of the Peverell brothers.
JK Rowling's assertion that she sometimes included a "throw-away detail" from a ghost plot in the books indicates that ghost plots do not necessarily fit neatly into the canon versus non-canon dichotomy. One of these "throw-away details" was Harry overhearing Dean Thomas explain that he did not know whether his biological father was a wizard or not because he left when Dean was a baby. The ghost plot that was cut would have had Dean discovering that his biological father was a wizard and why he left. Thus, it made sense for JK Rowling to include a remnant from a known ghost plot in the book. The part of the ghost plot where Dean discovers the truth about his father is not canon because, according to the conversation in Harry Potter and the Deathly Hallows, Dean doesn't discover the truth about his father.
Not all known ghost plots were removed because they were peripheral to the main story. Arthur Weasley's death was removed from Harry Potter and the Order of the Phoenix because JKR decided she wanted one of the few good fathers in the books to live. The removal of this ghost plot did not shorten the story since the circumstances which may have caused Arthur's death — a bite from Nagini while he was hidden in the Hall of Prophecy at the Ministry — remained intact. The need to cover up the circumstances under which Arthur was bitten would exist whether he lived or died, so would Sirius Black's explanation to the Weasley twins as to why they could not see their father, who might be dying, until after the hospital contacted their mother.
Removing Arthur's death plot did mean that, not only did any reference to Arthur being dead needed to be scrubbed from the rest of the series, but that Arthur also had to make at least an appearance in other books — meaning that he had to be written in and given things to do or say. It is not know whether JK Rowling invented a part for Arthur in subsequent books from scratch or whether she borrowed bits and pieces of storyline for him originally assigned to other characters.
Sometimes JK Rowling took questions concerning the books either before a particular ghost plot had been removed or while momentarily forgetting that it had been removed. Subsequently, she admitted on Pottermore that when she said something in an interview that did not match the book, it was due to a ghost plot.