I'm not too informed on villains, but I'll add my speculations.
I notice that Bill Cipher appears the most often of all the villains in people's lists. Reading about him, and seeing a video on Cipher vs Sans, Cipher is understandable, and might perhaps be one of the most powerful villains of all time.
I keep seeing Thanos and Darkseid as well. I found this interesting, but not surprising, as both are powerful beings.
There are many villains who are seen at least 3 times, but who I found most interesting was Godzilla. I found it rather surprising, since it is a GIANT dinosaur that can shoot lasers out of its mouth and all, coupled with really hard armor for a skin, but it can be defeated quite easily compared to some of the other villains.
Also interesting to see on the list was the 2008 Opera Version of The Joker. He is very manipulative, and is completely psychotic and apathetic. However, once you get to the Joker himself, he becomes quite easy to take down.
Galactus appears quite a bit, and seeing as he can chow down planets in one go, that's understandable.
Lord Voldemort appears quite a bit, to my surprise. Many people would probably know at this point that Voldemort is very weak compared to other villains of his like, such as Giygas and even Slenderman (though that's left up to debate).
Emperor Palpatine appears a lot as well. Considering what he has done, it's only slightly greater than that of Darth Vader and Lord Voldemort. Thus, I'm surprised that people mention him.
Unicron is also mentioned as well enough times. Unicron is quite powerful, so...
That's it for now.