General Terms
canon: the "official" source material upon which fanfiction is based.
fandom: a group of people that share interest in the same media (ie: story- harry potter, character- sirius black, etc.).
fanon: facts or situations that are widely used and accepted by fanfiction writers and readers.
fanzine: a collection of fanfiction produced as a magazine.
filing off the serial numbers: making a piece of fanfiction of copyrighted material suitable for publishing by removing any specific references to canon. (This might happen with extreme AUs.)
Abbreviations/Acronyms
AU/AT (Alternate Universe/Alternate Timeline): story that makes major changes to canon storyline or premise, such as killing off a major character or placing the characters in a high school.
A/N (Author's/Note): created when the author wants to explain something.
Gen (General): gen fics tend to lack a specific focus/genre (ie: angst, humor, romance).
H/C (Hurt/Comfort): where one character experiences pain (physical or emotional) and the other character offers comfort.
IC (In Character): the behavior of characters which seems logical, given what canon has supplied.
OC (Original Character OR Other Character): character created by the author of the fanfiction.
OTP (One True Pairing): two characters that the author is sure are destined to be together. This often goes against canon.
POV (Point Of View): perspective in which the story is viewed or written.
PWP (Porn Without Plot OR Plot? What Plot?): indicates that the story contains little or no plot. These stories are often (if not always) pornographic in nature.
R&R (Read & Review): encouragement from the author for the read to read the story and review it afterwards.
RPF (Real Person Fiction): written about real people- actors, musicians, athletes.
SI (Self-Insertion OR Self-Insert): a story in which the author writes him- or herself into it.
TWT (Timeline? What Timeline?): used when the author has no particular timeline that the story takes place during.
UST (Unresolved Sexual Tension): the lack of of full or partial resolution of sexual tension in a story.
WAFF (Warm And Fuzzy Feeling(s)): applied to stories which are intended to invoke those feelings in the reader (ie: "feel good" stories). Also referred to as "fluff."
Subgenres based on relationship to canon
alt: stories that are alternate versions of a specific section of canon. If the story was written before the book came out, it is referred to as "Pre-[Section of Canon]." If the story was written after the book came out, then it is considered to be a form of alternate universe; stories like these are sometimes written because the author dislikes what happened in canon, such as the death of a favourite character.
crossover: either characters from one story exist in or are transported to another story's world. Characters from two or more stories interacting is more common.
dark: plots which introduce elements such as death, violence, and betrayal.
movieverse: the film adaptations of books, games, etc.; the term is used to mark stories which are exclusively based on the movie.
pastiche: fan-produced parodies of published established works (ie: Hardware Wars, Troops)
uberfic: kind of alternate universe in which characters or events are portrayed closely to canon, but in a different time period (ie: ancestors, descendants or reincarnations of canon characters).
virtual seasons: usually a collaborative effort to produce a compliation of fan stories or scripts portraying espisodes of an entire season for a television program. This happens often with shows that have been canceled or no longer air episodes.
Subgenres based on character relationships
alternate pairing and "shipping": centered on characters who are not involved or seen as involved in canon. Pairings are also known as "ships."
het: a romantic and/or sexually explicit work focusing mainly on a heterosexual relationship.
lemon: stories without much plot other than sex. Also referred to as PWPs.
lime: stories that have sexual themes but are not necessarily explicit.
slash: term referring to same-sex pairings, sometimes exclusively male/male pairings. Lesbian pairings are often referred to as "femslash" or "femmeslash."
Other subgenres
crack!fic or acid!fic: characters are put in random or nonsensical situations, most often acting out of character.
fluff: a story that is devoid of angst and gives a light-hearted mood on romance.
religious fic: the primary character or characters experience an emotional crisis and adopt religious beliefs not mentioned in canon, usually those of the writer.
songfic: author take an exisiting song and uses its lyrics to generate the theme of the story or add emphasis to certain parts of it.
Other
name smooshing: alternative way to denote the pairing (ie: Severus Snape/Harry Potter = "Snarry").
If I left something out, comment and let me know!