Gunslinger: Like V said, at first there was no explanation, though in the Silver Age Lois Lane DID always suspect Clark and kept coming up with all kinds of zany schemes to prove it! (and Clark kept coming up with even weirder ways to disprove it- he even once got PRESIDENT KENNEDY (who knew his secret ID) to stand in for him (disguised as Clark!) Still, two canonical attempts to explain this away were: that Supes was (unconsciously) using his super-hypnotic vision (yes, that was one of his powers back then!) to keep people from noticing the resemblance; Post-Crisis, the public simply believed Superman had no secret identity at all (they thought he came to Earth as an adult and lived in his fortress) so no one looked for it. Even Luthor refused to believe it when a computer suggested the possibility, because he couldn’t see someone as godlike as Superman bothering to live among mortals!
I should also mention that (at least in the Silver Age) Superman & co. just kept running into people who looked just like him, from the first Metallo to his kryptonian cousin Van-Zee. I guess he just had “one of those faces!” 
OK, let’s see who’s left in my to-do list…
The Master Jailer: This villain was interesting in two ways: first, because he was a master of super-traps; and the other- because he was, in fact, a childhood friend of Clark Kent! (Sure, we already had Luthor in that role, but Luthor was retroactively inserted in Smallville, as mentioned early in this thread, while Carl Draper was invented that way from the start.)
Draper was one of those obese kids with little self-confidence who had a crush on a girl but never dared to admit it. And that girl was Lana Lang, who of course had a crush herself on Superboy, making Carl resent him, not realizing he was fellow nerd Clark. Ironically, Carl first became a villain because of Superboy; the Boy of Steel decided he needed something to “stay on edge” so he created Kator, a superpowered android programmed to challenge him. You can probably guess how well that went, and Superboy was forced to destroy it in the end; but Kator was smart enough to pass his powers and program onto Carl, and as a second Kator, he almost beat Superboy, but thankfully an emergency switch Clark had given Pa Kent (in case Kator went rogue) still worked on Carl (don’t ask me how) and he lost his powers and forgot all that had happened.
Years later, now an (actually handsome) adult, Carl had become an inventor fascinated by locks. He built a superprison to house Metropolis’ supervillains, complete with devices that drained their powers. His hope was that the publicity from the jail’s inauguration would impress Lana (whom he still pined for); unfortunately, Superman decided to make it safer by making it airborne; as a result the publicity went to him (they even renamed it Superman Island!) Infuriated, Carl used special “keys” he had invented to give himself the powers of three villains in the prison (Metallo, Parasite and Atomic Skull) and, under the costumed identity of Master Jailer, used them to capture Superman and imprison him in the “Island”. He also brought in Lana, trying to force her to be his girlfriend, but she smartly played along until she could free Supes. Draper ended a prisoner in his own jail.

(Note: Master Jailer should not be confused with The Key, a Justice League villain with a similar motif.)
Draper reappeared Post-Crisis, now called “Deathtrap”. I don’t know if he had any relationship with Lana now, but he already had a daughter, Carla. Draper creates the Deathtrap identity (smartly using a hologram so he can be in two places at once) just to prove he could capture and hold Superman… which of course he fails to do. In a humorous twist, Carla herself also becomes a villainess (“Snare”) behind her father’s back (apparently they are both unaware of each other’s secret!) and battled Superboy. Later, the spy agency CHECKMATE somehow discovers Carl’s secret and forces him to work for them as The Castellan, designing their security systems.
Silver Banshee: One of the first truly new villains invented for Superman after the Crisis, the Banshee was really Siobhan McDougal (uh, how do you pronounce that?) a member of a Scottish clan that had a secret ritual to prove who deserved to be their leader. Against the wishes of her uncle, Siobhan attempts the ritual but because of his interference, she’s dragged to some sort of Celtic netherworld. There, a being known as The Crone offers to release her if she can recover a book her father owned. She also turns the young woman into a scary being with supernatural powers: The Silver Banshee!

As you can guess, the book was in Metropolis, and Banshee started killing people to find it. And when Superman showed up to stop her- she KILLED HIM!! Well, sorta. You see, Banshee has the power to kill anyone with her scream, provided that she knows his or her correct identity. This seemed to work on Superman, but afterwards, the villainess was apparently haunted by Superman’s ghost, who was immune to her scream!! (It later turns out that Supes had survived her attack and was just in stasis for a while, and the “ghost” following her was really THE MARTAIN MANHUNTER, who was making clever use of his shape-shifting and intangibility powers to pretend to be Superman’s ghost- which not only psyched the villain out, but protected him since she didn’t know who he really was!
It turns out that the book was actually in Gotham City and Batman finds it and gives it to Superman. He takes it back to the Scottish island where the whole thing began, and The Crone takes it, dragging Banshee AND her uncle back to the underworld. (note: The Crone may have really been Blaze- see below.)
For a while, Banshee existed as an actual ghost, possessing people in an attempt to escape her damnation, but later comes back to life (as does everybody in comics sooner or later). She joined Luthor’s villain group. She was also seen in some episodes of the Justice League cartoon.
Silver Banshee is an interesting villain, but her power makes her a little too deadly. Not to mention Supes is already too weak to magic. She makes a better villain for other heroes.
Lord Satanus and Blaze: Two of the many demon lords in the DC Universe. They’re actually half-human brother and sister (their father being the wizard SHAZAM, the guy who gave Captain Marvel his powers!! He was tricked by a demon in disguise in his younger days.)

Although I mention them together, they are not allies, but rather rivals, as they try to steal human souls and gain enough power to rule Hell. Possibly because they are half-human, they come and go from the infernal realms as they please. They get involved with Superman mostly because Satanus has a thing for Metropolis (in fact posing as a local millionaire) and once even helped save the city! (after Luthor demolished it while he was dying.) Blaze, as mentioned above, once managed to ensnare the just-“dead” Superman’s soul (something about her ruling the Realm of Souls Who Refused to Accept their Deaths or something) but he was saved by Pa Kent’s soul.
Recently the two siblings did join forces to take over DC’s version of Hell from Neron, but Blaze (of course) betrayed her brother at the last minute, and now rules by herself.
Note: Lord Satanus may be a post-Crisis version of Lord Satanis, a sorcerer from the future who fought Superman a few times and also had to duel a female sorceress, though in his case it was his wife, Syrene. I sincerely hope this isn’t true because going from Husband-And-Wife to Brother-And-Sister is pretty… icky, even if in both cases they HATED each other.
Conduit: Ok, this guy is a REALLY special case. Like Master Jailer, he’s someone from Clark Kent’s past: Kenny Braverman, a boy born in Smallville at the exact moment Superman’s spaceship landed! Somehow, this affected him (perhaps because of the kryptonite chunk in the ship? Yeah, I know how the Smallville TV show has many people gaining powers from kryptonite, but in the comics that was rare.) Kenny became a star athlete but always overshadowed by- Clark Kent!? (Yep, post-Crisis, Clark was no wimp until he moved to Metropolis and had to hide that he was Superman. Note that his powers grew gradually, so he wasn’t cheating.) Kenny’s own father made things worse by focusing too much on his son’s “failures”.
Kenny grew up to become a CIA agent but had one of his missions also screwed up by Clark! He resented him so much that, when his powers manifested (he had to wear a special suit to contain and focus them- thus the name) he tried to kill Clark! This leads to his accidental discovery that Clark was really Superman; this drove him even crazier since he was convinced that Clark had always been cheating. He starts stalking Clark, threatening his friends and loved ones (did I mention he had kryptonite radiation powers?) and in the end duels the hero, but his own powers overloaded and (conveniently enough) killed him.

Kenny also appeared in episodes of Superman: TAS, so I kept wondering if he would ever turn into conduit, but he never did.
Kenny is the anti-Superman: from his origin to his powers to his attitude to the way he was raised. Although it was a bit gimmicky how his origin and Clark’s are connected, he was an interesting character, but by having him learn Superman’s secret they ended up needing to kill him off. Kenny also filled the part of the evil-character-from-Clark’s-past that Luthor and Master Jailer had before the Crisis.
Livewire: Livewire is a case of a character going from the 90’s Animated Superman series to the comics rather than the other way around. Livewire was a female “shock jock” who had it in for Superman for some reason; after being hit by a lightning bolt, she turned into a pale-skinned, blue haired person with electrical powers. She then decides to become a villainess;

It should be noted that Livewire and her powers (especially the ability to turn into electricity) resemble the powers Superman himself had for a while! In (yet another) publicity stunt for the Superman titles, they actually had some kind of accident change his powers (and costume) for about a year’s worth of comics (he still called himself Superman, though.) It turned out that he was secretly hosting an alien energy being, Kismet, who later would find another host, a young woman, who became the heroine “Strange Visitor.” Livewire might be a reference to this storyline. Also, note that Lightning Lad (of the Legion of Superheroes) went for a few years under the name “Livewire” as well, and he has a sister with similar powers who also kinda looks like the animated Livewire.)
Livewire proved popular enough (probably because Superman has so few female foes) that they actually teamed her up with Batman’s own female fatale duo, Harvey Queen and Poison Ivy, to battle- Supergirl and Batgirl! I’ll bet that was a popular episode with teenage boys! 
Livewire was eventually introduced in the comics (where it was revealed she already had the latent (metahuman) ability to manipulate electricity, but it was only when hit by the bolt that it fully activated, which makes more sense.) She actually helps save the world from an alien who came to Earth to steal all the metahumans.
Manchester Black: This guy deserves mention for being created basically to help prove to modern fans why Superman, with his old mores and values, still rocks. Apparently based on a member of the Authority (a popular independent comic superhero group famous for literally busting heads to get the job done) as were the rest of his team, Manchester was a British guy with tremendous psionic powers. His team, The Elite, went around the world killing villains, saying it was a more effective way of handling them and deriding Superman for his moral limitations.

Finally, after much prodding, Superman challenges all of them to a battle (that gets televised around the world). Shockingly, Supes then proceeds to KILL ALL THE ELITE MEMBERS, ONE BY ONE, saving Manchester for last!! Only then he reveals he had only pretended to kill the others, using his powers in clever ways. But he makes his point: if he’d WANTED to kill them all, he could have. Is that really what they –and the World- wanted him to be? The World was very happy he wasn’t.
Manchester however, only got angry at the hero, and came back later. He was dead set on proving that Superman was a fake… instead, after failing to break Superman even after trapping him in an illusory world where his worst nightmares (such as Lois dying) came true, Manchester realized HE was the real villain, and committed suicide. (Another case of a Superman villain who had to die ‘cuz he knew the hero’s secret identity.)
Manchester has a sister, Vera, with similar powers, who becomes a hero and joins a branch of the Justice League to redeem her brother’s name.
Superboy Prime: Saving the worst for last- sorry but this guy just pisses me off. Or his current version does anyway.
Hark back to 1985 and the Crisis on Infinite Earths. Since part of the plan was to have every character ever published by DC to appear in that story, especially if they were going to be erased from the continuity, someone decided Superboy had to appear as well. Except, Superboy was Superman when he was a boy, so, wouldn’t that meant he had to know the Crisis was coming? The way they got around it: they introduced Superboy as coming from another Parallel Earth… and for some reason, they chose Earth-Prime, the Earth without heroes (or villains) I mentioned above under Ultraa. Turns out the Clark Kent of that world had never developed superpowers for some reason, until the chaos of the Crisis activated them. Superman ran into the fledgling Superboy and actually took him under his wing, motivated by his recent loss of Supergirl (killed by the series’ villain, the Anti-Monitor.) Superboy-Prime actually helps the Superman from Earth-2 to kill the Anti-Monitor, but appears to be killed by the cosmic being’s death-throes. In fact, the two Supermen were rescued by Alexander Luthor (son of the Luthor and Lois of Earth-3) whose dimensional powers bring them to another dimension they could “never escape, but which was a paradise”; he’d already brought the Lois of Earth-2 (Superman-2’s wife) there. Obviously, the writer’s intent was to give these characters a better ending than just “killed off” or “erased from history” like so many other characters in the Crisis were.
Zip to 2005: In the sequel, Infinite Crisis, the four characters mentioned above return from their “limbo” to help fix the new universe that had replaced the Multiverse at the end of the first Crisis. Except it turned out that they WERE behind a lot of the terrible things that were happening (except for Superman and Lois, who didn’t know what Alex and Superboy were really up to.) Apparently years of living in “paradise”, able to see the real world but not affect it, drove them insane. Superboy ends up fighting several heroes AND KILLING THEM, mostly by tearing them apart with his own hands! He even KILLS THE ORIGINAL SUPERMAN!!! (Lois had died just before of old age apparently.) Alex meanwhile manages to recreate the universe but is killed by the “real” Luthor and the Joker. Superboy-Prime is depowered and held prisoner by the Green Lantern Corps.
I hate, hate, HATE this series. It was basically a big “You though we were REALLY going to make the DC Universe less dark, didn’t you? HA-HA!” to fans like me. And it started the use of the gratuitous dismemberments, decapitations and other gross stuff that still show up unpredictably in DC Comics, and are the reason I don’t buy their comics anymore. As for Superboy Prime? He’s now back to being ultra-powerful (remember, he has the same power levels that Superman had BEFORE the Crisis, so he can literally shatter worlds!) AND he’s all-out evil. And yes, he has killed more people. I blame writer Geoff Jones (who wrote Infinite Crisis and keeps bringing his perversion of Superboy Prime back) and DC President Dan Didio for allowing this to happen. After that wonderful finale 20 years ago, they bring back the characters just so Superman-2, THEIR FIRST SUPERHERO EVER, can be beat to death? These people have no respect for the characters. Or their fans. >:(
Note: Superboy-Prime should not be confused with Ultraman, the evil Superman from Earth-3.
….AAANND that’s all, folks! Oh of course there’s tons of Superman villains I haven’t mentioned (he’s been published since the 40’s after all!) but I think I covered all the meaningful (or interesting) ones. Your opinion may of course differ.
After writing this article, I can only conclude that the reason so many of them are so poorly known is that they haven’t been handled well, or given appropriate publicity. Just look at all the Batman villains who have appeared in his movies: sometimes two or more at a time! But with Superman, it’s ALWAYS Luthor (to the point of making Emo Luthor a fan-favorite character in teenage Superman’s own TV show!!) Seriously if they had bothered on using more characters from the comics in the Superman movies, they might be more popular. (At least the 90’s cartoon did a good job of introducing many of them to the younger generations.)
Hope you have enjoyed this retrospective. I certainly had fun writing it, And reading your comments! (You are welcome to post more here if you wish.
) Until next time….