Possibly Secrecy Sensors and Sneakoscopes
I would argue that Secrecy Sensors can detect Polyjuice Potion. First, it would make sense given the description of Secrecy Sensors in Chapter Fifteen of Half-Blood Prince:
"Look", sighed Hermione, "Secrecy Sensors detect jinxes, curses, and concealment charms, don't they? They're used to find Dark Magic and Dark objects.
While a concealment potion may be different from a concealment charm, the purpose of the Sensors is to detect concealment so it would be reasonable that they detect potions as well.
Furthermore, the Sensors appear to be the only security check applied to students in Half-Blood Prince. From Chapter Eleven:
Well, Filch ran over all of us with Secrecy Sensors when we got into the entrance hall.
If Secrecy Sensors could not detect Polyjuice Potion then it would seem that there would have been nothing preventing a Death Eater from entering Hogwarts disguised as a student. Considering that Hogwarts had already housed a Polyjuiced Death Eater for an entire year, failure to check for this would have been gross negligence (though this is Dumbledore we're talking about).
More importantly, there is potential evidence from Barty Crouch Jr. (disguised as Mad-Eye Moody). In Chapter Twenty of Goblet of Fire he introduces Harry to his Dark Detectors, one of which was a Secrecy Sensor:
"What's that?" Harry asked, pointing at the squiggly golden aerial.
"Secrecy Sensor. Vibrates when it detects concealment and lies... no use here, of course, too much interference – students in every direction lying about why they haven't done their homework. Been humming ever since I got here.
Note that he mentions that Secrecy Sensors can detect lies, which was not mentioned in their description in Half-Blood Prince. We also never find anyone using Secrecy Sensors when they want to determine if someone is lying, though there were a bunch of opportunities for this throughout the series. Furthermore, we find that throughout Half-Blood Prince Filch was able to use a Secrecy Sensor without having any problems with interference (and presumably there was no significant change in the homework-lying habits of students in the two year interim).
I would therefore argue that Crouch Jr. lied to Harry about the Secrecy Sensor. The Sensor was clearly activated when Harry was there, which required an explanation:
In the corner on a small table stood an object that looked something like an extra-squiggly, golden television aerial. It was humming slightly.
Since neither of them were ostensibly engaging in jinxes, curses, concealment charms, or Dark Magic, Crouch had to come up with an alternate explanation, so he blamed it on students lying about homework and Harry fell for it. In truth, though, the real reason why it was humming was that it detected that Crouch Jr. was impersonating Mad-Eye Moody.
Similarly, Crouch Jr. explains that his Sneakoscope has been whistling non-stop:
I had to disable my Sneakoscope because it wouldn't stop whistling. It's extra-sensitive, picks up stuff about a mile around. Of course, it could be picking up more than kid stuff," he added in a growl.
Compare this to the description provided in Chapter One of Prisoner of Azkaban:
If there's someone untrustworthy around, it's supposed to light up and spin.
Throughout the rest of Prisoner of Azkaban the Sneakoscope is constantly acting up, and they assume that it's broken. However, I would argue that it was actually picking up Peter Pettigrew pretending to be a pet. Consider that in Harry's house it seemed to work fine:
Harry put the Pocket Sneakoscope on his bedside table, where it stood quite still, balanced on its point, reflecting the luminous hands of his clock.
And in Goblet of Fire (Chapter Twenty-Three) it seems to have gone back to working fine:
The reason they were extra-knobbly was that Harry had been using them to cushion his Sneakoscope for over a year now. He pulled out the Sneakoscope and handed the socks to Dobby, saying, "Sorry, I forgot to wrap them..."
Thus, before and after being in the presence of Pettigrew the Sneakoscope worked fine, and it only didn't work when Pettigrew was around. This seems indicative of the fact that it was not actually broken, and was actually detecting Pettigrew's untrustworthiness.
I would therefore argue that Crouch's Sneakoscope was similarly picking up on the fact that he was impersonating Moody, and because he couldn't tell this to Harry he made up another excuse about why it was acting up.
Based on the above, I think it is possible that there are certain magical objects – such as Secrecy Sensors and Sneakoscopes – which could detect that someone is impersonating someone else via Polyjuice Potion. However, it would seem that they do not actually confirm that the specific method is Polyjuice Potion; you would still have to figure out yourself that that was what the instruments were detecting. And they also do not actually reverse the effects of the Polyjuice Potion. But merely knowing that there is some trickery or concealment involved would often be enough. If the instruments detect something you could confine the suspect until the possible potion would wear off, or you could decide to question the suspect in such a way that would confirm the impersonation.