David Lean worked with Alec Guinness on six movies- starting with Great Expectations in 1946 and concluding with A Passage to India in 1984.
M. Night Shyamalan used Bruce Willis twice, then Joaquin Phoenix twice, then Bryce Dallas Howard twice.
That’s because after the actors have worked with him twice, they realize he’s a self-centered twit and won’t work with him anymore. 
John Turturro is part of at least two stables- he appears in loads of Spike Lee’s movies as well as loads of Adam Sandler’s.
In Sandler’s case, however, he’s rarely the director of his films- he usually has someone like Dennis Dugan as the nominal director.
Neil Labute and Aaron Eckhart.
Hal Hartley and Martin Donovan.
Turturro also appeared in several Coen Brothers films.
And Johnny Depp has done several with Gore Verbinski (the Pirates of the Caribbean films, Rango and The Lone Ranger).
It make sense to me. If you’re an actor, comfortable with a director and you find success in his or her films, you’re going to willing to work for him or her again.
James Cameron and Pill Paxton, Michael Biehn and Arnold Schwarzenegger.
Edgar Wright and Simon Pegg, Nick Frost and Martin Freeman.
…none of whom have major roles in The Avengers.
Bzzt! Denisof is Thanos’ lackey.
But I’m not sure of your point since The Avengers was built as a showcase for the main characters from five previous films that Whedon had nothing to do with.
I just agreed to go see Pacific Rim again with friends - in which Ron Perlman is working again with Del Toro. I suspect I know what the topic of conversation before the movie begins will be…
Although some of the stars of The Avengers may now have joined the Whedon Posse: Clark Gregg was in Much Ado About Nothing and will be in the new Agents of S.H.I.E.L.D. TV series. Also, Chris Hemsworth was in The Cabin in The Woods, which apparently led to him getting the title role in Thor (and therefore also being one of the stars of The Avengers).
I admit, for the first few minutes of Much Ado About Nothing I was a bit distracted: “Oh, look! It’s Fred! And Wesley! And Agent Coulson! And Simon Tam! And…” But I got over it pretty fast.
I remain astonished that Enver Gjokaj doesn’t get more work, but full marks to Whedon for stretching the guy nine ways from Sunday.
Plenty of examples listed here. 
Herzog/Kinski anyone? Bueller? Klaus Kinski was reportedly worse than impossible to work with, but Herzog insisted on him whenever he could.
I’m well aware of that–it’s why I specified “major role.” Denisof isn’t even recognizable in the film. And it is perfectly relevant, since this thread started out talking about the upcoming Avengers sequel and how Joss Whedon’s tendency to use the same actors makes his movies less interesting. Obviously he is perfectly capable of working with other sets of actors, since the Avengers was a generally well-acclaimed film.
Jim Jarmusch has a few people he likes to use in his films.
ETA: interesting trivia: Founder member of “the Sons of Lee Marvin”. Other members include Tom Waits, Thurston Moore, John Lurie Nick Cave. Membership requires a plausible likeness to Lee Marvin such that you could be rumored to be his son.
I knew I got that term from somewhere!
Aww… I hadn’t heard that Napier died. Still he appeared in loads of Demme’s movies, from early efforts like Citizen’s Band (aka Handle With Care) through The Manchurian Candidate.
Paul Thomas Anderson often works with the same stable of actors, many of them taken from Mamet’s stable.