Although it also came 20 years before the term was coined, 1965's The Great Race, set in Edwardian times with an evil mad scientist and a multitude of wacky inventions, can also be considered a Trope Codifier.
The 1960 and 2002 adaptations of The Time Machine. Especially the 2002 version—its "star" has a Difference Engine under the readout dials.
In the Casper feature film, the mansion's secret laboratory. The rest of the film, sadly, doesn't have the attitude.
Doc Brown's time-locomotive at the end of Back to the Future Part III: "It runs on steam!". Another example earlier in the movie was his steam-powered refrigerator (which was big enough to take up a garage by itself).
The film Mutant Chronicles is firmly entrenched in the steampunk genre, though it forgoes zeppelins in favour of flying trains. It actually looks more plausible than it sounds.
Van Helsing is set in the 1890s and features all sorts of steam punk gadgets used to fight monsters. Notably an automatic crossbow and switchblade stake are used to attack vampires. Frankenstein's monster is given a steam punk design in this too.
The movie version of A Series of Unfortunate Events shows the heroes encountering a number of Victorian-esque adventurers who have since settled into retirement—as well as gotten themselves marked for death by Count Olaf.
Young Einstein is a deliberately In Name Only biography of the original with him as a Tasmanian apple farmer who invents atomic powered beer as well as dates Marie Curie.
In Terry Gilliams' The Brothers Grimm the brothers wear steampunk-esque uniforms and use steampunky scientific instruments which really don't do anything, as they are con men.
The 1970s Czechoslovak detective comedy Adele Hasn't Had Her Dinner Yet features a lot of steampunky gadgets and esthetics both on the side of the protagonists and the bad guys, given that it's an Affectionate Parody of turn-of-the-century pulp novels and penny dreadfuls.
The 2012 film Tai Chi Zero is a fictional retelling of how Tai-Chi first got taught to the outside world. The antagonist of the film wants to bring modern (19th century) ways to the village - including a giant steam-powered railway-laying machine. The sequel, Tai-Chi Hero, continues the tale.
The Geographer's Guild in Paddington with its pneumatic archive tube system.
The second fantasy sequence in Sucker Punch takes place in a World War I inspired setting - where the girls must combat German soldiers that have been resurrected by steam punk technology. Blondie and Rocket also have steam punk themed costumes.
Treasure Planet features a really interesting fusion of steampunk and cyberpunk, merging steampunk-style culture, aesthetics, and physics with cyberpunk-level technology.
Atlantis: The Lost Empire has some aspects of steampunk in the beginning, considering that in 1914 the characters travel to Atlantis in a submarine so technologically advanced at least in design and features that it hasn't been made 95 years on. Oh, and, the giant drill truck. Then again, this is the film that contains flying fish-like craft powered by crystals full of Applied Phlebotinum, so...
The Boxtrolls features the rickety car driven by Snatcher and his men and the contraptions built by the titular boxtrolls. Not to mention the massive Spider Tank Snatcher operates in the finale.
The French-Canadian-Belgian film April and the Extraordinary World (Avril et le Monde Truqué) is set in an alternate world where many of the world's best scientists have disappeared over the years, stalling the world's technological progress so by 1941 the world is still trapped in the Steam Age. The movie takes a more realistic view of a world still using steam power; a Crapsack World where, after the world's coal resources have been depleted, the French government has started strip-harvesting Europe's forests to provide power, and is now preparing for war against North America to control the forests of Canada. The skies are perpetually gray and sooty, and black lung disease is implied to be fairly common.
Mythica: Admiral Borlund Hess and her Sky Pirates have a steam-powered air ship and a "war wagon" (essentially a steam-powered automobile).