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Edited into 

Austin Powers: The Spy Who Shagged Me (1999)
Footage is used during the rocket launch.

References 

Buck Rogers (1939)
line "No bucks, no Buck Rogers".
Marooned (1969)

Referenced in 

NewsRadio: Goofy Ball (1995)
Beth: "Houston, we have a problem"
The Red Green Show: The Tax Refund (1996)
Unable to figure out what's going on during Possum 911, Red exclaims, "Houston, we have a problem!"
Mystery Science Theater 3000: The Incredible Melting Man (1996)
"It's the same crap from Apollo 13"
Father Ted: Tentacles of Doom (1996)
A character says he saw this film recently and it reminded him of his own brush with death.
The Simpsons: Bart on the Road (1996)
Lisa says, "Houston, we have a problem. Homer 13 is spinning out of control!"
Very Important Pennis: Very Important Pennis: Part 1 (1996)
Dennis mentions this when talking to Tom Hanks, who is at the Venice Film Festival to promote this film.
Scream (1996)
When Stu discovers that the gun is missing, he says "Houston, we have a problem".
Fathers' Day (1997)
Drive (1997)
Mystery Science Theater 3000: Prince of Space (1997)
Tom (as the "church of the bomb" explodes): "They never even had the time to tell Houston that they had a problem."
RocketMan (1997)
Mad About You: The New Friend (1997)
Ira mentions this film and the famous phrase: "Houston, we have a problem."
Slappy and the Stinkers (1998)
Domino comments that the "launch" is just like Apollo 13 and that he and his dad saw the film 3 times. After the leaf blower flies off by itself, he comments "Houston, we have a problem".
Mystery Science Theater 3000: The Phantom Planet (1998)
Mike: Houston, we have a moron.
The Simpsons: This Little Wiggy (1998)
Bart says, "Houston, we have a booger!"
Quest for Camelot (1998)
Cornwall says "Houston, we have a problem"
Armageddon (1998)
Max: "Houston, we have a problem!" Harry: "Houston, you have a problem!"
The Directors: The Films of Roger Corman (1999)
Mentioned by Ron Howard.
Terror Firmer (1999)
"Houston, we have a problem."
The Simpsons: They Saved Lisa's Brain (1999)
Homer says, "Houston, we have a problem - a sexy problem!"
American Pie (1999)
During the internet scene, after Jim 'blows it' one character says "Houston We have a problem!"
Bats (1999)
Jimmy: "Houston, we've got a problem"
Toy Story 2 (1999)
Red Planet (2000)
Spy Kids (2001)
During the airplane ride, a console light comes on saying "Main Bus Undervolt"
How to Make a Monster (2001)
The line "Houston, we have a problem."
The Shipment (2001)
"Houston, we got a problem."
Stranded (2002)
Coupling: The Girl with One Heart (2002)
Listing various ways to describe a serious problem, Jeff includes, "Houston! Forget that other thing".
Saturday Night Live: Elijah Wood/Jet (2003)
Referenced in Queer Eye
Tripping the Rift: Ghost Ship (2004)
Mentioned by 'Leonard Nimoy'
Physics in Your Life (2004)
Mentioned by Professor Wolfson in Lecture 11.
The Butterfly Effect (2004)
There's a poster of this film at the cinema.
King of the Hill: Stressed for Success (2004)
Kelly Clarkson lists celebrities info
Top Gear: Episode #4.4 (2004)
Jeremy mentions the film Apollo 13
Scooby-Doo and the Loch Ness Monster (2004)
When Shaggy and Scooby are falling through the air in the van, Shaggy says "Houston, we have a problem".
The Amazing Race: Houston, We Have an Elephant (2005)
Uchenna and Joyce see an elephant of their drive, Uchenna exclaims "Houston we have an elephant."
How It Should Have Ended: How Saving Private Ryan Should Have Ended (2005)
"I suppose next you are going to tell me you were in the Apollo 13 mission"
Pitbullterje (2005)
Movie poster seen in Jim's room.
ER: Man with No Name (2005)
Morris says ''Houston, we have a problem''- this line was made famous by the movie Apollo 13
Jeopardy!: Episode #22.35 (2005)
correct response in "Movie Taglines" category
Desperation (2006)
Ron Perlman quotes the film.
The Office: The Job (2007)
Michael says "Houston, we have a problem"
St. Trinian's (2007)
"Houston, we have a problem"
Be Kind Rewind (2008)
Video case is shown.
CSI: NY: Playing with Matches (2008)
Mac quotes "Houston, we have a problem"
Who Wants to Be a Millionaire: Episode #7.22 (2008)
Included in a $2,000 question
The Kevin Bacon Movie Club (2008)
movie with Kevin Bacon
Phineas and Ferb: Out to Launch (2008)
Phineas says, "Danville, we have a problem."
Night at the Museum: Battle of the Smithsonian (2009)
Clint Howard as a NASA mission controller
Who Wants to Be a Millionaire: Episode #7.166 (2009)
Included in a $16,000 question
Transformers: Revenge of the Fallen (2009)
Bumblebee plays a clip of Tom Hanks saying, "Houston, we have a problem."
G.I. Joe: The Rise of Cobra (2009)
Ripcord says "Houston We've got a problem", when he doesn't find any buttons to fire in the Night Raven
Making of 'Vorstadtkrokodile' (2009)
The members of the band Apollo 3 report they viewed this movie and came up consequently to their band name
Planet 51 (2009)
Baker says, "Houston, we have a little problem!"
Jeopardy!: Episode #26.85 (2010)
Subject of a $1,200 clue in the category "Ron Howard Films"
Saturday Night Live: Charles Barkley/Alicia Keys (2010)
Quote is a question during 'Reel Quotes'
Sherlock: A Study in Pink (2010)
Sherlock calls, "Houston, we have a mistake!"
Sherlock: Unaired Pilot (2010)
"Houston, we have a mistake"
Cougar Town: You Don't Know How It Feels (2010)
mentioned in dialogue
Cougar Town: Fooled Again: I Don't Like It (2010)
mentioned in dialogue
Top Gear: Episode #16.6 (2011)
Mentioned by James while in the Rover II
NCIS: Los Angeles: Rocket Man (2011)
"Houston, we have a problem." quote by Eric.
Saturday Night Live: Alec Baldwin/Radiohead (2011)
Taran Killam thought Apollo 18 was a sequel to this film.
The Vampire Diaries: Disturbing Behavior (2011)
"Houston, we have a problem"
Revenge: Guilt (2011)
"Houston, we have a problem"
Tosh.0: Face Bumper Smash (2011)
"Houston, we have a swallower"
Family Guy: Back to the Pilot (2011)
"Houston, we have a solution"
Face Off: Return to Oz (2012)
poster seen
Bering Sea Gold: After the Dredge: Gains and Losses (2012)
Ian mentions the title, and the box/hose/duct tape part

Features 

Bewitched (1964)

Featured in 

The Universal Story (1995)
clip shown
The Manchurian Candidate (2004)
Footage shown of special effect of Saturn 5 rocket at politcal convention.
AFI's 100 Years... 100 Movie Quotes: America's Greatest Quips, Comebacks and Catchphrases (2005)
The quote "Houston, we have a problem." is #50 on the list.
20 to 1: 50 to 01: Great Movie One Liners (2007)
Some clips from this movie are shown in a segment on the line "Houston, we have a problem."
The Jay Leno Show: Episode #1.88 (2010)
a clip is shown in a montage of Bill Paxton's films
The Tonight Show with Jay Leno: Episode #19.63 (2011)
a clip is shown in a montage of Ron Howard films
The Tonight Show with Jay Leno: Episode #19.158 (2011)
a clip is shown in a montage of Kevin Bacon films
Late Show with David Letterman: Episode #19.2 (2011)
Altered clip of Tom Hanks presented as a greeting on Dave's 18th anniversary show

Spoofed in 

Casper: Rocket Booster/A Really Scary Casper Moment/Day of the Living Casper (1996)
In "Rocket Booster", Casper's telling of when he went into space is spoofs the events in Apollo 13.
Mystery Science Theater 3000: Laserblast (1996)
Mike parodies the famous line "failure is not an option" in one sketch.
Spy Hard (1996)
Married with Children: Grime and Punishment (1997)
Kelly, enacting the history of the USA: "Houston, we have a problem. I can see Uranus."
Dante's Peak (1997)
Plump Fiction (1997)
Titanic (1997)
Home Alone 3 (1997)
The Wrong Coast (2004)
The movie "Apollo the 13th", is a cross and parody of "Apollo 13" and "Friday the 13th".
Garfield (2004)
Garfield's quote "Houston we have a problem" while playing "astronaut" is a parody of the line from Apollo 13.
Disaster! (2006)
the fuel suddenly drops to Empty: "Houston, we have a problem."
The Big Bang Theory: The Classified Materials Turbulence (2009)
Wolowitz dumps out a box of spare parts available on the International Space Station required to fix his zero-G toilet much like the Mission Control people did to make a new carbon dioxide scrubber
The Haunted World of El Superbeasto (2009)
a drunk astronaut says "Houston, we no longer have a problem."
Community: Basic Rocket Science (2010)
Abed's story of not being able to take the trip to "space" and needing to help the crew to get back to Greendale spoofs Gary Sinise's sub plot in the movie; the crew getting rescued out of the caravan at the end is similar to the Apollo-crew landing safely back on earth and being welcomed back by a crowd of people in the movie
Mater's Tall Tales: Moon Mater (2010)
The Impala XIII radios back to Earth: "Houston, I have a problem!"

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