X-Men: One of five uncredited writers; only two punchlines are actually Whedon's, including a non sequitur by Halle Berry which probably wasn't funny even as scripted. The storyline for X-Men: The Last Stand also adapted several elements and plot points from his run on Astonishing X-Men, most notably the character of Dr. Kavita Rao and the concept of a mutant 'cure'.
Serenity: Continuation of the aborted Firefly series, with an actual budget this time. Mal (Nathan Fillion) and co. discover a few skeletons in the Alliance's closet which, if broadcast to the media, may loosen their grip on the population. Meanwhile, the Alliance dispatches an Implacable Man to retrieve River Tam (Summer Glau).
Buffy the Vampire Slayer: A semi-sequel to the feature film, with Buffy (now Sarah Michelle Gellar) fleeing L.A. and going underground in a sleepy suburban town to the south. Unbeknown to her, the town also rests on the mouth of Hell. D'oh. Launched the majority of what is known as the Buffyverse.
Angel: A spinoff of the Buffy series, starring David Boreanaz (Bones) as Buffy's vampire ex-lover who continues to fight demons, with hopes of becoming human in the bargain. In contrast to Buffy, Angel's foes tend to represent financial and political evils.
Firefly: Space cowboys, adrift in a bucket of bolts, go on adventures while eluding The Man — In this case, an enlightened, milquetoast society which does a lot of nasty things in secret to maintain power.
Dollhouse: Ex-convicts, runaways, and lost souls volunteer to become empty vessels for the shadowy Rossum Corporation, who in turn implant various personalties into their bodies. One such "Doll", Echo (Eliza Dushku), pretends to cooperate with her bosses in hopes of getting her old personality back.
Action Girl: Very common. Though Whedon himself doesn't think this should even be a trope. He once recounted how interviewers always ask why he writes so many strong, competent female characters, saying he always wants to yell at them about why they aren't asking every other writer why they don't write these kinds of characters.
To elaborate, instead of viewing a character as a woman who does "action-y" things, view it as a character who does "action-y" things who happens to be a woman; the emphasis lies on the actions of the character and not the gender.
Anyone Can Die: Villians, heroes, children, the main character, anyone can die in a Joss Whedon production.
Buffy / Angel: Jesse, Jenny Calendar, Doyle, Tara, Anya, Joyce, Lilah (sorta), Cordelia, Fred, Wesley, Lindsey, Spike, Angel, and Buffy herself, twice. Giles as well as of the Season 8 comics.
Firefly / Serenity: Shepherd Book, Wash.
Dollhouse: Topher Brink, Boyd Langton, Paul Ballard, Mellie!November, Bennett Halverson, and possibly the majority of the cast considering the Distant Finales.
Atheism: Whedon is rather hardline about this, but on the other hand, he is capable of writing religious characters without letting his own beliefs influence him. Steve "Captain America" Rogers in The Avengers, for instance, is given a line wherein he states his belief that "There's only one God", but that's pretty much the only thing the other Avengers don't make fun of him for. And Shepherd Book is shown to be a friendly, open-minded Christian as well as a deep, well-rounded character.
Author Appeal: Likes to give a few of his characters English accents (Joss attended school in Britain), like The Watchers, Spike, Adelle, and that Badger fellow.
People with mental illness shows up in a lot of his shows.
Buffy Speak: While he didn't invent it, Joss and his shows had a big hand in changing the way TV and movie characters talk, especially white teenagers. This isn't because he likes it so much as it's how he speaks.
Dropped a Bridge on Him: Though he's always had a reputation for using Anyone Can Die, he's lately been accused of relying on it a bit too much, killing characters off just for cheap shock value long after we've learned to suspect it's coming.
Family Business: Membersof the Whedon family have been writing for television practically since the medium's inception, and then, of course, there are his brothers.
Foot Focus: Before there was Echo, there was River ... and Drusilla. And Fred. And Eve. And Lilah. And Pepper.
Foreign Cuss Word: A staple of his productions. Examples include Spike dropping a British cuss words on Buffy, the Serenity crew swearing in Mandarin, and Loki calling Black Widow a "mewling quim" in The Avengers.
Hollywood Atheist: Malcolm Reynolds is deeply bitter against God/Christianity after losing a war. Nathan Fillion himself stated that Mal is actually a Nay Theist who's pissed off after the Serenity Valley.
Whedon himself is an interesting case. He says he can't bring himself to believe in a god, but he's actually very bothered by that.
Never My Fault: A few people have notice how it always seems to be someone else who messed up a project he's on.
Old Shame: The unaired Buffy pilot. It's on Youtube if anyone's interested. Also, the film.
Whedon was asked by IGN Film Force in June 2003 about the unaired presentation:
IGNFF: Is the presentation ever going to make it to DVD? Whedon: Not while there is strength in these bones. IGNFF: Well, I mean, it's one of the most heavily bootlegged things on the Internet. Whedon: Yeah. It sucks on ass. IGNFF: Yeah, it does, but it's sort of that archival, historical perspective... Whedon: Yeah, I've got your historical perspective.
Carlos Jacott, best known for shooting Bill Henrickson in the finale of Big Love, played the smarmy villain Ken in the Buffy episode "Anne". He would later appear on Angel ("Bachelor Party") and Firefly ("Serenity").
Jane Espenson, who wrote for Buffy (including the comics), Angel, and Firefly. Joss made a cameo in her series Husbands.
Put on a Bus: Numerous characters, but most notably Kitty Pryde during his run on Astonishing X-Men. Particularly shocking, considering how much he loved the character ( she's often cited as an inspiration for Buffy). Obviously, another writer undid it. But still...
Too Happy to Live: Whedon regularly kills happy characters, or destroys their lives, or ruins their relationships.
Took The Bad Film Seriously: He wrote Alien Resurrection as a satirical parody, in an attempt to get fired from the job. The studio executives instead thought the script would make a perfect action / horror film. invoked