In Backstreet Dreams, Dean and Manny frequently refer to themselves as Butch and Sundance.
The Way of the Gun: The names of the main characters— Parker and Longbaugh— are the real-life last names of Butch and Sundance.
The film's director George Roy Hill referenced it in his later 1979 film A Little Romance, in which the French boy Daniel is a fan and watches it (dubbed into French) in a local Paris movie theater.
During the climax of Beverly Hills Cop, Rosewood mentions the climax of this movie to Taggart during a shoot-out.
You know what I keep thinking about? The end of Butch Cassidy, where Newman and Redford are almost out of ammunition and the Bolivian army is right outisde this little hut.
In Mallrats, the silent mall cop is named La Fours, to the point of wearing a straw hat. This was nodded to in a conversation between Jay and Brodie that was deleted, but can be seen on the extended edition DVD:
Jay: Is La Fours out there?
Brodie: No.
Jay: Good. For a minute there, I thought we were in trouble.
In On the Buses, apon seeing Vera and Ruby, the depot's first two frumpy female bus drivers, Stan calls them Butch Cassidy and the Sundance Kid.
In Boot Camp, the kids at Lake Harmony are made to say that they'd be dead if not for camp. Garrett sarcastically says to Adam, "Let me guess. You'd have gone out in a hail of bullets. A regular Butch Cassidy and the Sundance Kid."
The Patagonia Special in Top Gear nods back to the film a couple times thanks to Jeremy Clarkson's love of it. Not only does Jeremy attempt to recreate the bicycle scene, but the special also ends with a remake of the film's Bolivian Army Ending (playing off of the cast and crew being driven out of Argentina by a mob), right down to using the same audio track during the freeze-frame.
The West Wing: An episode of the second season is called "The Fall's Gonna Kill You", and when Josh tells C.J. that President Bartlet and Leo are worried about the perception they will have only disclosed the President's MS because of a poll Joey Lucas put in the field, C.J. points out they're acting like Butch and Sundance right before they're about to jump off the cliff.
At the end of "Duffless", Homer and Marge ride a bicycle into the sunset while singing "Raindrops Keep Fallin' on My Head".
A 1994 syndication promo, which has the Simpsons rotoscoped into various movie moments, has Homer and Bart recreating the cliff-jumping scene from this movie.