Maybe ihis is more coincidence than inside joke, but in Season 4 of his show, when Angelus jokingly suggests that they offer him a bribe to cooperate, he mentions that "the new Mustangs are really nice, and what's a better ride than a Mustang?" David is, himself, a fan of the Ford Mustang, and owns a classic 1965 convertible.
(These two might not technically qualify, since they're on non-Whedon shows, but they DEFINITELY poke fun at Whedon's characters)
Also, in one episode of "Castle," Fillion dresses up in his Mal Reynolds outfit from "Firefly" and "Serenity", complete with brown coat and handgun, as a "Space Cowboy" for Halloween and when a murder victim (complete with puncture wounds in the neck) is discovered in a cemetery, says "Buffy must be off tonight."
And on "Smallville," in a Season 5 episode, there is a college sorority, all vampires, run by "Buffy Saunders."