Abusive Parents / Parental Abandonment: A staple of the Jossverse, sometimes lampooned. For the Freudians out there, Joss' parents split before he turned 10. Though he does speak well of both his father and stepfather, saying both helped shape his feminist views.
Amusingly, by season 3 of Angel this reached the point where the fact that Fred's parents were perfectly nice people came off as a shocking twist.
Action Girl: 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. 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.
Anyone Can Die: Villains, 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, particularly Mr. Dominic and Ivy.
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 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.
And now, Pepper.
Foreign Cuss Word: A staple of his productions. Examples include Spike dropping 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 Naytheist 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.
Whedon: The idea of doing [The Avengers] three times just staggers the imagination. I’m not that young. But then, I hadn’t really intended to do a second one. In the third one, I really am going to kill everyone.
Loads and Loads of Characters: On his commentary for The Avengers, he laments that both feature films he's directed suffer from this problem, meaning a few will inevitably not get the focus they deserve.
Mood Whiplash: Many heartwarming scenes and jokes in Whedon works are followed by a character being unexpectedly and often brutally murdered seconds late and many a very dramatic scene will be punctuated with a joke.
The unaired Buffy pilot. It's on Youtube if anyone's interested. Also, the film.
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.
Nathan Fillion, Mal in Firefly, Caleb in Season 7 of Buffy and Captain Hammer in Dr. Horrible
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
What Could Have Been: A particularly potent one, for comic books fans and companies alike: before he was attached to The Avengers, Whedon was writing a Wonder Woman movie for DC. DC passed on it, he got the Avengers job from Kevin Feige, and the rest is history. Imagine how much DC must be kicking themselves.
Whedon ultimately cast his Wonder Woman as SHIELD agent Maria Hill, and she did get to play the character, eventually.