The public at large wouldn't know Gul Dukat from a seagull.
Unlike Vader, Khan was never a henchman. He was the bad guy in two previous Trek installments.
Harry Mudd appeared in three Treks. Q in several episodes over three different series.
You missed my point. I only brought up Dukat because he was the closest thing there was to a true recurring nemesis, which has nothing to do with how popular he is. My point about Vader is that he became over emphasized among fandom as the baddest villain, something that STID has done with Khan's importance.
Dukat's only seems "truer" because of the serial nature of DS9. The ones I mentioned are true recurring nemesis as well. Species like the Klingon, Borg and Romulans count too, even though they aren't individual characters.
Boba Fett is a better candidate of a character taking off in popularity, who really does nothing. He's pretty much the poster child for that. Vader's popularity might be why he becomes Luke's father in Empire and tries to take over in Jedi. He's a cool visual, which is why he's bigger than the Death Star on the posters. He's also the guy who captures Leia and kills Ben. So I think he's a little bit more than a henchman. He's probably as important as Tarkin to the film's villainy.
STID calls Khan the "baddest villain" because he's the villain in STID. They aren't going to have Spock say, "Yeah, he's bad news. But there's this other guy who's worse. Lucky you're not facing him."