They have a different kind of power.
House-elves are not necessarily more powerful than wizards, but they do have a different kind of magic. Because elves are frequently demeaned and looked down upon by wizards their powers are underestimated by most wizards.
“And his knowledge remained woefully incomplete, Harry! That which Voldemort does not value, he takes no trouble to comprehend. Of house-elves and children’s tales, of love, loyalty, and innocence, Voldemort knows and understands nothing. Nothing. That they all have a power beyond his own, a power beyond the reach of any magic, is a truth he has never grasped."
(Deathly Hallows, Chapter 35, King's Cross).
Duels between elves and wizards were very rare indeed. Remember that Dobby was a particularly rebellious elf to start off with. Most elves wouldn't dare to resort to violence against a wizard, and certainly not their master. So most wizards wouldn't have an opportunity to see how able elves are to fight and would logically presume that their magic is limited to cooking the dinner and other menial tasks. See how shocked Bellatrix is, for instance, when Dobby fights back against her and her family.
“Kill him, Cissy!” shrieked Bellatrix, but there was another loud crack, and Narcissa’s wand too flew into the air and landed on the other side of the room.
“You dirty little monkey!” bawled Bellatrix. “How dare you take a witch’s wand, how dare you defy your masters?”
(Deathly Hallows, Chapter 23, Malfoy Manner).
House-elves are certainly able to hold their own against wizards if push comes to shove. Rowling even says that they have certain powers that wizards don't have.
Rorujin: How is Dobby able to Apparate inside Hogwarts if no one else can?
JK Rowling: He's a house-elf, they've got powers wizards haven't got (but wizards have also got powers that house-elves haven't).
(World Book Day Chat, 2004).
As for the confrontation between Dobby and Lucius, it's probable that it was more than simple magical power that drove Lucius away.
But Dobby shouted, “You shall not harm Harry Potter!”
There was a loud bang, and Mr. Malfoy was thrown backward. He crashed down the stairs, three at a time, landing in a crumpled heap on the landing below. He got up, his face livid, and pulled out his wand, but Dobby raised a long, threatening finger.
“You shall go now,” he said fiercely, pointing down at Mr. Malfoy. “You shall not touch Harry Potter. You shall go now.”
Lucius Malfoy had no choice. With a last, incensed stare at the pair of them, he swung his cloak around him and hurried out of sight.
(Chamber of Secrets, Chapter 18, Dobby's Reward).
Lucius probably knew that attacking and killing Dobby wasn't really a viable option in the middle of a school, especially when Dumbledore had just uncovered his involvement in the opening of the Chamber of Secrets. So Lucius not having a choice to fight back may be more a matter of what he could get away with socially rather than what he was able to do magically.
We do see that Kreacher is able to track down and subdue Mundungus Fletcher so it is clearly possible for a house elf to do this. So they clearly do their own magic which they are able to use against wizards when they want to. This is wandless magic but that isn't so remarkable; we see wizards doing wandless magic too (the wand just channels the magic).