Heartland: A recently widowed man, struggling to survive on his isolated homestead, sends away for a mail order bride. Married as strangers, together they must edure great hardship, tragedy, and skeletons wielding swords as they farm the land.
Flightplan: Jodie Foster is a propulsion engineer who panicks when, mid flight, her daughter disappears. No one is willing to believe her: Her daughter has been kidnapped by skeletons wielding swords.
Stealth: Fast paced action ensues as three hotshot pilots push their skeletons wielding swords to the limit against an all new, experimental foe: A rogue computer-controlled skeleton wielding a sword.
I may be waaaay off on this one, but in the movie “Young Sherlock Holmes,” there’s a hallucination sequence in which some characters from a stained glass window (and other places?) come to life and start attacking Holmes. I think one of them may well be a sword-wielding skeleton. Those special effects, incidentally, are, I believe among the first to use CGI.
An argument could be made that Revenge of the Sith has a skeleton wielding a sword. General Grievous is some sort of cyborg who IIRC had some exposed bones, and he wielded four light sabers.
(Continuing on the "Any movie is made better with skeletons with swords line of thought) Spoilers for Serenity…
In the last act of the movie, the Serenity crew has to fight an onslaught of Reavers, a spacefaring race of canibalistic skeletons with swords. The Operative is also a skeleton with a sword, albeit a much cooler one.
Easy Rider — Cap’n America and Billy are just about to be attacked by the meanest rednecks you ever saw, when the sword-wielding skeletons jump out and slash the tires on their pickup to ribbons.
Yellow Submarine — An army of blue skeletons wielding swords tries to hack the Beatles to shreds, but John starts singing “All You Need Is Love” and the skeletons’ swords turn into flowers with tendrils twining around them, through them, and out their eye sockets.
Jacob’s Ladder — Jacob is pursued on the subway by a band of nightmarish vibrating demons with no faces, but the undercover transit security guys throw off their trenchcoats and pull off their masks, and lo! they are sword-wielding skeletons who bayonet the demons in the gut.
As noted above, Harry Harryhausen’s Seventh Voyage of Sinbad was the one where he first did it. I don’t know of any examples before that (although there were many cartoons of skeletons before that – but I can’t think of any with swords). Harryhausen then used the same idea in the aforementioned Jason and the Argonauts. It was a tour de force in animatio. Think f all the limbs moving , each in their own direction and at their own speed. Then try to imagine keeping track of all that in your head. Harryhausen did all the anmation himself. (He also did a seven-headed, two-tailed hydra in th same film. In one scene, it’s carrying a dead body that had to be animated, too. The mind boggles)
Harryhausen didn’t use skeletons after that, although he did use very skeleton-like fghouls in Sinbad and the Eye of the Tiger. (There was a skeleton in Clash of the Titans, but it wasn’t animated.
Spy Kids 2 is practically a tribute to Harryhausen – they had to throw in the skeletons, even though they don’t make much sense. The hybrid beasts are more appropriate. (And did anyone ever mention that they’re all puns – a Hore-fly, a Spider-monkey, etc.)?
Likewise Army of Darkness. Two generations of moviemakers have grown up watching Harryhausen.
Eraserhead: You remember the scene where Jack Nance’s head falls out of a window into the street. You haven’t seen the scene they cut that explains how it happened: He was attacked from behind by sword-wielding skeletons!
Twin Peaks: The Man from Another Place is seriously fucking with Dale Cooper’s head. He has him running from one red-draped room to another without being able to tell which room he’s really in. BOB is about to infest Cooper’s soul. Then the sword-wielding skeletons slash down all the red curtains, leaving a big open space, allowing Cooper to escape.
Mulholland Drive: Two women are making love. One of them is about to go down on the other when she shrieks as she sees an army of miniature sword-wielding skeletons marching out of the other woman’s vagina. It’s inexplicably blue. They chuckle with glee and kill her.