Just about everything in Armageddon goes wrong, but they somehow manage to destroy the asteroid anyway. Put briefly, the Russian Space Station explodes for no reason just after they refuel, one shuttle is destroyed by debris and crashes (but Ben Affleck survives), the other crashes on an almost undrillable section of the asteroid, Steve Buscemi goes crazy with Space Dementia and starts shooting at everybody, the President almost decides to detonate the nuke prematurely and then doesn't, the asteroid kills more people with geysers, but the transmitter on the nuke was deactivated, forcing Bruce Willis to make a Heroic Sacrifice.
Inglourious Basterds: Subverted, and gloriously so. While there are some bumps along the way (Three quarters of the Basterds dying before the plan is even underway, for example), it's very satisfying seeing all three plans to kill Hitler succeed. Subverted in another way as well, since the main one was only in danger of failing because they got involved.
Pretty much the MO of Lawence Block's accidental secret agent Evan Tanner. Faced with a ridiculous surfeit of problems (uncover a Soviet plot at the Toronto World's Fair, avoid the Canadian authorities, rescue his adopted daughter, foil an assassination attempt on the Queen of England, dispose of a quantity of heroin) he works them out on the fly with little more than connections, friends and quick thinking.
The breaking into Godwin Arms and Armaments in the Science Fiction novel Profiteer by S Andrew Swann. The Heroes have been betrayed, so the enemy knows they are coming, but they somehow pull it off anyway.
Happens frequently in the Harry Potter series, particularly in the last book, where the trio spend roughly a month planning the break-in of the Ministry of Magic, and then another month planning the break-in of Gringotts. In both cases, they focused on getting in, and overlooked things that might happen while they were inside. Neither goes according to plan, but they still pull it off anyway, both times.Lampshaded in the film version, with regard to the upcoming infiltration of Hogwarts, which they didn't have time to plan for anyway.
They actually show us what the perfectly-performed plan looks like, too, and even mislead us a little into thinking it's the actual performance of the plan, with the characters narrating/explaining their parts. This makes the blunder-filled version that much more hilarious. And exciting. (Of course, this is the common inversion of the Unspoken Plan Guarantee: since we hear the plan, you know it won't go that smoothly in practice.)
Many missions in the Grand Theft Auto series don't go as planned. Bank robberies and drug deals are particularly prone to failure. The more straightforward the mission seems, the more likely someone will botch it up or betray you and leave you running for your life.
Star Wars screencap webcomic Darths & Droids: in their version of Episode One, the entire Tatooine plot arc was just a giant Gambit Roulette performed by Qui-Gon Jinn purely by accident. He made so many stupid mistakes that they came full circle and canceled each other out. Summarized wonderfully here.
Scooby-Doo embodies this trope so often, it would be easier to note when it doesn't.
Scooby-Doo, Where Are You'' episode, "Nowhere to Hyde" featuring the Ghost of Mr. Hyde.
The Scooby-Doo Show episode featuring Mamba Wamba.
Done on the PBS children's show Clifford the Big Red Dog, when Clifford tries to catch Vaz's attention away from the latter's TV binge by hopping around outside. Instead, Clifford wrecks the satellite dish by accident, causing Vaz to go investigate. However, he sees Clifford outside, so Clifford successfully gains his attention despite the failure of his original plan.
Done frequently in The Dreamstone. A lot of times, Rufus and Amberley's attempts to stop the Urpneys fell short or led to their capture. They always ended up with the Dreamstone back however, given the Urpneys were perfectly able at screwing up their plans on their own
The Iron Man: Armored Adventures episode "Field Trip", where Tony, Pepper and Rhodey's plan to get the armour back without Stane noticing only comes off at all thanks to interference from Gene, Happy and Stane's daughter.
Pepper: Well, that went perfectly. Apart from everything.
The assassination of Franz Ferdinand. To wit, all the assassins were supposed to throw grenades, fire pistols, then drink cyanide and drown themselves in the river. Instead, all but one of them froze up, and the one who acted missed with both bullets and grenades and wasn't even successful in killing himself. (The cyanide had lost its potency and the river was too low to drown in—he was arrested immediately). Later that day, one of the guys who didn't shoot was walking out of a sandwich shop—probably feeling guilty about his massive failure—when the Archduke's driver got lost and wound up right in front of him. This time, he didn't freeze.
Dwight D. Eisenhower once stated that, "In preparing for battle, I have always found that plans are useless but planning is indispensable."