Bane suffers in fan memory partly due to the undeniable influence of the Poochy Effect. He was specifically designed by his creators with one goal in mind: to be Batman's Doomsday. In theory, he should be a mess, but just as I have a soft spot for Doomsday, I think Bane is one of the company's most underutilized characters.
For all that people complained about Doomsday, he was the perfect villain for his story: an irrational, wrathful force of nature with no real motivation other than hatred, he was the living embodiment of everything Superman had sworn to fight. So what if he was grown in an editorial test tube and plopped down into an event storyline that culminated in one of the most egregiously hyped events in an egregiously hyped era of comics? So what if he was the spitting image (no pun intended) of all the worst excesses of the Chromium age - that was clever satire, whether intended or not. The squarest superhero of all up against a monster from the darkest recesses of Rob Liefeld's id. It was fun and holds up a hell of a lot better than, say, Bloodstrike or The X-Cutioner's Song. Superman got to go down fighting the good fight in the most unambiguous, blatantly heroic way conceivable. That was Doomsday's purpose, and for that he did an admirable job.
Building a better Batman villain was always going to be a trickier prospect. It had to be someone who represented - like Doomsday for Superman - some kind of polarized opposite who could take Batman apart with the same ease. The whole point of the exercise, after all, was to ultimately redeem the heroes by providing a situation against which their "old fashioned" heroic ideals could ultimately triumph - providing an explicit rejoinder to all the crappy copycats clogging up the stands during the period. (The real battle in the last part of the Knights saga, after all, was not a rematch between Batman and Bane but between Batman and the Punisher-lite Azrael.) Just as Doomsday was a cartoonish, over-exaggerated creature of pure menace, the ultimate monster for the ultimate hero to slay, Bane needed to represent a similar kind of iconic challenge to Batman - and because, like, Doomsday, he was only needed for the first act of the overall story arc, he could be as monstrously efficient as possible without necessarily stretching credulity.
So: what was - is - Batman's greatest attribute? More than anything else, what has always been Batman's greatest super-power?
Bane, regardless of his origins, is a truly great villain because he was the first (that I can recall) who was ever smart enough to use Batman's greatest strength against him. I recently went back and re-read Knightfall and was pleasantly surprised by just how well it held up. It's a really solid story: for months leading up to the event, Bane was a secretive presence on the outskirts of Batman's world, gradually lining up adversaries and manipulating events in such a way as to keep Batman running through hoops to the point of exhaustion. FInally, just when seams began to show in Batman's powerful facade, he lowers the boom: he demolishes Arkham Asylum and lets loose every single one of Batman's worst foes. After this, Batman has no choice: he has to push himself to the limits of endurance and beyond in order to capture every single one of these madmen. He's driven, but he's only a man and he can't take the strain. Batman successfully overcomes every obstacle Bane throws in his path, but all the while Batman knows there's something else out there, something waiting for him, something with the mind to set the entire city on fire for the single purpose of running his chosen prey through the most taxing gauntlet of his life. Suddenly, Batman is afraid.
And Bane knows this. He knows that Batman is too brave, too willful, too defiant to ask for help - he knows that Batman wouldn't just get on the JLA horn and call for Superman's help. He knows that Batman, when pushed, will isolate himself from his friends and family. He also knows that Batman is not a creature of magic or endowed with superhuman endurance: if pushed long and hard enough, he will eventually reach his absolute limit. And when it's time, Bane is there, waiting for Bruce Wayne when he returns home to Wayne Manor, reaching out with his big meathook hands and crushing Batman with all the effort it would take to break a ragdoll. That's all it takes, and Batman is done.
After that, it's no real surprise that Bane fell into disrepair. It's even explicitly addressed in the story: once you've broken Batman, what's left? He has no real interest in crime for its own sake, he's not a thief by nature or a sociopath. He is simply the physical incarnation of WIll, but with no direction he was useless. A lackey, a pawn, a mercenary - none of these really fit, but there wasn't anything left for him to do. No one since then - with the exception of Gail Simone - has really figured out what Bane should do, since he already accomplished the one impossible task he initially set out to do. It doesn't matter that he eventually got beaten by Azrael, it doesn't matter that he's been humiliated in the years since. The fact is, he hasn't half been trying since he broke the Bat. And in his heart of hearts, Batman knows this.
This is what keeps him up late, with cold sweat curling down his back. Not psychotic killers, not amoral gangsters, not grotesque monsters - it's that eyeless mask, the so-simple-it's-inescapable luchador mask that seems to encapsulate every hateful emotion ever felt. Batman knows that, when the chips were down, and when Bane truly put his mind to it, he was able to take Batman apart like a cheap watch.
The only thing that gives him any comfort at all is that, for the longest time, Bane hasn't had any real goal, any real direction to channel his seemingly limitless will. What scares Batman the most, more even than the Joker or Two-Face or Zsasz or Darkseid, is the thought of what Bane could do if he ever really put his mind to it.
The Penguin is the greatest Batman villain for the simple reason that he's the meanest. He's not crazy, he's not super-strong, he's not endowed with any real overriding mania or fixation. He has motifs, yes, but ultimately he's perfectly sane. He doesn't go to Arkham, he goes to real big-boy jail.
What the Penguin has that no one else has is a simple abundance of pure, unadulterated spite. He's a short man with a paunch and a beakish nose. He's been picked on and derided and underestimated his whole life, dismissed by his social betters and spit on by women. He's ruthless and cunning and amoral because those are the cards life dealt him.
I admit I'm not the biggest fan of his current status quo: the evil-nightclub-owner-slash-gangster routine has been stale for a while, because it essentially neuters him by turning him into a static threat. He has a base of operations but no real active agenda anymore. That should change: the Penguin should be out and about, stirring shit up and hatching master plans. When the Joker steps into a room, you know he's going to kill you just because he's crazy; but when the Penguin steps into the room you know it's because he has a reason to be in that room, and if you are in his way he will not hesitate for one second to pop open a trick umbrella and shoot your kneecaps. He might not kill you just for the sake of killing you but he knows how to make you wish you were dead if you ever cross him. He's cold, cruel and calculating. He's resourceful and cunning, because that's how you get ahead in the world.
In Batman's world there's madness, obsession, will and strength - but ultimately it all comes back to crime, pure and simple. The Penguin's motivations are pure because he simply resents the whole damn world and will not rest until he gets his. The Penguin is a criminal, nothing more and nothing less, with avarice in his heart and hatred in his eye.